Rep. Peter King (R-N.Y.) heads to the Capitol Building for a vote on March 2, 2011 in Washington, D.C. (Ricky Carioti/WASHINGTON POST)

A Republican congressman who examined radicalization among American Muslims urged the Justice Department on Monday to explain what he says was its decision to “usurp” the prosecution of a Muslim advocacy group on terrorism financing allegations.

Rep. Peter T. King (N.Y.) said he had been “reliably informed” that high-level Justice officials in the Obama administration chose not to seek indictments against the Council on American-Islamic Relations (CAIR), its co-founder and two other Muslims groups. He said the decision was made despite vehement objections from FBI agents and prosecutors, who wanted to pursue the case.

“Their opposition to this decision raises serious doubt that the decision not to prosecute was a valid exercise of prosecutorial discretion,” King said in a letter to Attorney General Eric H. Holder Jr. dated Friday and released by the congressman’s office Monday.

A law enforcement official familiar with the case said it was Justice officials in the George W. Bush administration who initially decided not to charge CAIR co-founder Omar Ahmad.

The official, who spoke on the condition of anonymity to discuss internal deliberations, said the Obama administration then rejected a subsequent effort to bring charges against Ahmad. The official declined to specify the reasons for the decisions. Neither administration sought an indictment of CAIR as an organization.

Dean Boyd, a spokesman for the Justice Department, said in a statement that it brings cases based only on evidence and that “the notion that an individual suspect or organization is immune from Justice Department prosecution solely because of their affiliations, memberships or political leanings is not only false but an affront to Department prosecutors nationwide.’’

Ahmad, who is no longer affiliated with CAIR, did not return telephone calls Monday. It is unclear whether indictments were sought against the other Muslim groups named in King’s letter, the Islamic Society of North America and the North American Islamic Trust.

Safaa Zarzour, secretary general of the Islamic Society, said King has “an anti-Muslim agenda.” The North American Islamic Trust said in a statement that the group’s designation as an un-indicted co-conspirator in a terrorism financing case, which King’s letter cited, was “an intentional smear campaign.”

The debate over a case that was never brought illustrates the lingering tensions over U.S. Muslims and their relationship with law enforcement a month after King held a hearing exploring homegrown radicalization. The hearing, which came after a series of high-profile incidents linked to American Muslims, drew fierce condemnation from Muslims and civil rights groups.

CAIR, one of the nation’s largest Muslim advocacy groups, came under criticism at the hearing from some Republican congressmen, who called it a terrorist organization. They based the allegation on the Bush administration’s designation of CAIR, along with more than 200 other individuals and organizations, as an “un-indicted co-conspirator” in the terrorism financing case.

In that case, a federal jury in Dallas in 2008 convicted five men with ties to the Texas-based Holy Land Foundation for Relief and Development — once the nation’s largest Muslim charitable organization — of providing material support to Hamas. The U.S. government has designated Hamas as a terrorist organization.

Groups or individuals designated as un-indicted co-conspirators in a criminal case often are never charged.

After CAIR was given the designation in the Holy Land Foundation case, the FBI cut off official ties with the organization, which had been a key part of the government’s intensive outreach efforts to U.S. Muslims since the Sept. 11, 2001, terrorist attacks. In a 2009 letter to several U.S. senators, FBI official Richard C. Powers said evidence at the Holy Land Foundation trial demonstrated a connection between CAIR, “individual CAIR founders” and Hamas.

“In light of that evidence, the FBI suspended all formal contacts between the FBI and CAIR,” the letter said. CAIR officials say they still frequently talk to the FBI about civil rights cases.

CAIR has long denied any terrorist ties, and spokesman Ibrahim Hooper on Monday called King’s letter to Holder “an obvious attempt at political payback for criticism of the anti-Muslim bias in Mr. King’s recent hearing.’’

“It is sad that Representative King’s personal vendetta against the American Muslim community has led him to become a mouthpiece for anti-Islam hate sites,” Hooper said.

Hooper was referring to Pajamas Media, a conservative Web site that last week published a story accusing the Obama Justice Department of scuttling the case against CAIR for political reasons.

King, in an interview, said he was aware when he wrote to Holder that the Bush administration also had rejected indictments against co-conspirators in the Holy Land Foundation case. Asked why he was criticizing only the Obama administration, King said the difference is that Bush officials made their decision before the convictions in the case.

“Whether or not there is any criticism of Bush we can debate, but clearly there has to be criticism of Obama and Holder,’’ said King, a longtime critic of Holder who recently called for the attorney general’s resignation. “The rationale for not indicting was removed.”