The FBI is severing its once-close ties with the nation's largest Muslim advocacy group, the Council on American-Islamic Relations, amid mounting evidence that it has links to a support network for Hamas.

All local chapters of CAIR have been shunned in the wake of a 15-year FBI investigation that culminated with the conviction in December of Hamas fundraisers at a trial where CAIR itself was listed as an unindicted co-conspirator.

The U.S. government has designated Hamas as a terrorist organization.

An official at the FBI's headquarters in Washington confirmed to FOX News that his office directed FBI field offices across the country to cut ties with local branches of CAIR.

In Oklahoma, FBI officials had worked with CAIR's local branch from its founding in 2007 and attended the fundraising banquet that launched the office. But just over a year later, the local FBI froze all its programs involving CAIR.

FOXNews.com has obtained an Oct. 8, 2008, letter sent by James E. Finch, special agent in charge of Oklahoma City, canceling a session with local Muslim organizations "as a result of the planned participation by the Oklahoma chapter of the Council on American-Islamic Relations (CAIR)."

Click here to read the letter, which was provided by the watchdog group the Investigative Project on Terrorism.

The new policy marks a major shift for the FBI, which has long been close to CAIR. The agency has previously invited CAIR to give training sessions for agents and used it as a liaison with the American Muslim community.

CAIR's executive director, Nihad Awad, attended a post-Sept. 11 meeting with then-FBI director Robert Mueller, and he met with other top brass as recently as 2006. But that was before Awad was shown to have participated in planning meetings with the Holy Land Foundation, five officials of which were convicted in December of funneling $12.4 million to Hamas.

Click here to see the government's evidence in the Holy Land Foundation case.

Prosecutors identified CAIR's chairman emeritus, Omar Ahmad, as an unindicted co-conspirator in that trial, and Special Agent Lara Burns testified that CAIR was a front group for radical organizations operating in the U.S.

CAIR denies that it conspired in the case and has sued unsuccessfully to have its name removed from the list of co-conspirators. It also is protesting the FBI's decision to sever relations.

"This is an unfortunate legacy of the Bush administration's misguided and counterproductive efforts to marginalize mainstream American Muslim organizations," CAIR's national office said in a statement to FOXNews.com.

"It is not surprising that we would be singled out by those in the previous administration who sought to prevent us from defending the civil rights of American Muslims."

But not all CAIR branches have been told of the FBI's new policy.

"Locally we have not had any reports, we have no letters from the FBI to suggest that" ties were being severed, said Ahmed Rehab, a spokesman in CAIR's Chicago office. "It's a working relationship and that remains in place."

It remains unclear whether CAIR's national office is still in contact with the FBI, as a formal statement from the bureau seemed to hold out the possibility for renewed engagement.

"The FBI has had to limit its formal contact with CAIR field offices until certain issues are addressed by CAIR's national headquarters," said FBI spokesman John Miller. "CAIR's leadership is aware of this. Beyond that, we have no further comment."

CAIR keeps its headquarters in Washington and runs more than 30 offices in 19 states. But the national outreach programs that it once helped coordinate with the FBI may now be in doubt.

News of the split comes as President Obama has been reaching out to the Muslim community to build closer relations. Obama granted his first television interview as president to Al-Arabiya, an Arabic-language news network based in Dubai, a move widely interpreted as extending an olive branch to Muslims at home and abroad.

CAIR told FOXNews.com that it was hoping for improved ties with the new president. "We look forward to better relations with the Obama administration," the organization's D.C. office said in its statement.

FOX News' Mike Levine contributed to this report from Washington.