NEW YORK » The anxiety and anger have been building all year. In March, a national coalition of a dozen Islamic organizations warned that it would cease cooperating with the FBI unless the agency stopped infiltrating mosques and using “;agents provocateurs to trap unsuspecting Muslim youth.”;

In September, a cleric in Bay Ridge, Brooklyn, sued the government, claiming that the FBI had threatened to scuttle his application for a green card unless he agreed to spy on relatives overseas — echoing similar claims made in recent court cases in California, Florida and Massachusetts.

And last month, after an imam in Queens was charged with aiding what the authorities called a bomb-making plot, a group of South Asian Muslims there began compiling a database of complaints about their brushes with counterterrorism investigators.

Since the terror attacks of 2001, the FBI and Muslim and Arab-American leaders across the country have worked to build a relationship of trust, sharing information both to fight terrorism and to protect the interests of mosques and communities.

But those relations have reached a low point in recent months, many Muslim leaders say. Several high-profile cases in which informers have infiltrated mosques and helped promote plots, they say, have sown a corrosive fear among their people that FBI informers are everywhere, listening.

“;There is a sense that law enforcement is viewing our communities not as partners but as objects of suspicion,”; said Ingrid Mattson, president of the Islamic Society of North America, who represented Muslims at the national prayer service a day after President Barack Obama's inauguration. “;A lot of people are really, really alarmed about this.”;

There is little doubt that a spate of recent cases — from the alleged bomb plot by a former Manhattan coffee vendor, Najibullah Zazi, to the shootings at Fort Hood, in Texas — has heightened Americans' concerns about homegrown terrorism. Muslim leaders have promised to redouble efforts to combat extremism in their ranks.

Yet they also worry about the fallout for the vast numbers of the innocent. Some Muslims, Mattson said, have canceled trips abroad to avoid arousing suspicion. People are wary of whom they speak to. Community groups say it is harder to find volunteers. Many Muslim charities are hobbled.

And some law enforcement experts warn of a farther-reaching consequence: the loss of a critical early-warning system against domestic terrorism.

“;This is a national security issue,”; said David Schanzer, who heads the Triangle Center on Terrorism and Homeland Security at Duke University. “;It's absolutely vital that the FBI and the Muslim-American community clear the air and figure out how to work together.”;

Even in better times, the relationship has been a challenge to maintain, given that counterterrorism agents operate on multiple levels — holding open meetings at a mosque, say, and seeding it with informers.

The FBI has defended its practices, saying it must pursue suspects wherever they go. Paul Bresson, an FBI spokesman, said in an interview that it tries to resolve anxieties by giving community leaders “;explanations, where the circumstances permit, and resolving concerns where possible.”;

In October, agents met privately in Queens with more than 40 Muslim and Arab-American leaders to hear their grievances, and agency officials said they anticipated more sessions in New York and other cities. In July, Attorney General Eric Holder took questions about counterterrorism tactics from 200 young Muslims at a Los Angeles mosque.

Bresson said that no group is spotlighted because of its members' religion or ethnicity. “;The FBI investigates people, not places, and only when we have information or allegations that persons are or may be committing crimes or posing a risk to national security,”; he said.

Yet the Justice Department has in the last two years loosened some restrictions on agents' ability to start and conduct terrorism investigations. The new guidelines, which the FBI confirmed in October in response to a suit filed by the civil rights group Muslim Advocates, make it easier to plant informers and allow agents to include ethnicity and religion in the assessment of targets, as long as those are not the only factors considered.

After four members of a mosque in Newburgh, N.Y., were charged in May with plotting to bomb two Bronx synagogues, the authorities acknowledged that the investigation had begun with an informer who became a linchpin in the scheme. Congregation members said he had frequented the mosque, offering young men money and gifts.

The Queens imam arrested in September as investigators pursued the coffee vendor was an informer who had helped authorities. Last month, federal prosecutors moved to seize several buildings across the country that house mosques, saying they were owned by a nonprofit group with links to Iran. As a rare federal investigation that has ensnared houses of worship, the case stoked apprehensions that the government sees Arab-Americans and Muslims as a people apart.

“;We are citizens who care about our country as much as everyone,”; said Wael Mousfar, president of the Arab Muslim American Federation, a New York umbrella group. “;But people don't know what to expect — who might report them for speaking about Middle East politics, what someone might get your teenage son to do.”;

His community's relations with law enforcement were rocky in the weeks after 9/11, when the authorities began detaining hundreds of Muslim and Arab noncitizens, most of whom were cleared of links to terrorism and deported. But FBI officials and leaders of Muslim, South Asian and Arab-American groups eventually forged an understanding, maintaining communication channels.

Linda Sarsour, director of the Arab-American Association of New York, a social-services agency, said that even then, the connection felt tentative. She was baffled when bonds that she and other leaders established with a New York FBI chief evaporated upon the arrival of his successor.

Experts say that complaint partly reflects high turnover.

It also attests to differing views within the bureau about the effectiveness of community outreach, said Michael Rolince, a former director of counterterrorism in the FBI's Washington field office. Some factions within the agency, he said, have always been leery of Islamic and Arab-American organizations, considering their loyalties to be divided.

“;There are some people in the bureau who believe, as I do, that the relationship with the Muslim community is crucial and must be developed with consistency,”; Rolince said. “;And there are those who don't.”;

The American Muslim Task Force on Civil Rights and Elections, which threatened to cease cooperating with the FBI, has not yet done so.

But by most accounts, the unraveling of ties began two years ago, with the FBI's decision to stop sharing information with the nation's most prominent Muslim civil rights organization, the Council on American-Islamic Relations. The FBI said it was motivated by council executives' failure to answer questions about links with the Palestinian militant group Hamas. The executives denied any such connection, and accused the FBI of staining the council's reputation without due process.

In June, the American Civil Liberties Union made a similar complaint about Justice Department decisions to shut down six Muslim charities without filing charges. The moves, which froze billions of dollars in assets, have instilled among Muslims “;a pervasive fear that they may be arrested, prosecuted, targeted for law enforcement interviews”; if they give to any Islamic charity, the ACLU said.

Imam Mohammad Shamsi Ali, chief cleric at the Islamic Cultural Center of New York, in Manhattan, said that his organization had suffered a 30 to 40 percent decline in contributions since 2001, in part because of that fear. He said the center no longer solicits donations from individuals living abroad “;because of the possibility that we could be misunderstood.”;

Still, the specter looming largest among immigrant Arabs and Muslims is fear of deportation. And some say the FBI has used that threat forcefully.

Sheik Tarek Saleh, the Bay Ridge cleric who is suing the government, said he welcomed FBI agents at his storefront mosque after 9/11 when they asked about his kinship with Mustafa Abu al-Yazid, a high-ranking al-Qaida militant and his cousin's husband.

Sheik Saleh, 46, said he repeatedly discussed Yazid as well as his own former membership in the Muslim Brotherhood, a sometimes-violent political movement he joined as a teenager in Egypt and disavowed years later. But when he refused to travel overseas to spy on Yazid, he said, agents told him to forget his pending application for permanent residence.

In February, immigration officials told Saleh that the application had been rejected because he failed to fill in a section about ties to political groups. He contends that was a minor oversight. FBI and immigration officials would not discuss his case.

Saleh said that he faced deportation because he resisted FBI pressure. “;Your dignity is bigger than the green card,”; he said.

Zein Rimawi, a pet store owner and a founder of the Al-Noor School, a private school in Bay Ridge, said the anxiety has made people cautious about their transactions with individuals and institutions — even his school, which he said was $700,000 in debt as a result.

Rolince, the former FBI agent, said he understood the worries, but felt they were overblown. “;The FBI has 12,500 agents,”; he said. “;Believe me, there's not enough of them to waste time looking at you unless they have a good reason.”;