In September 2004, Rep. Joe Pitts (R-Pa.) received $2,000 from Zaheer Ahmad, who was active with a nonprofit Washington group known as the Kashmiri American Council.

The FBI now says that Ahmad was an unregistered agent of the government of Pakistan, whose role included funneling money to U.S. politicians. He is listed in the group’s records as a conduit for donations to lawmakers including Pitts, the FBI says.

The episode shows how Pakistan’s spy agency, the Inter-Services Intelligence, allegedly sought to influence Kashmir policy in Washington over the past 20 years, according to federal court documents filed in Northern Virginia this week. The FBI estimates that the foreign intelligence agency poured at least $4 million into campaign contributions, public relations campaigns and other efforts during that time.

Several weeks after the 2004 donation, Pitts introduced a resolution in the House urging the appointment of a special envoy to push for a peaceful resolution of the dispute in Kashmir, which has long been divided between Pakistan and India.

A Pitts spokesman said Wednesday that there was no connection between the donation and the resolution, and said the congressman was “very upset” by the allegations against the Kashmir council.

“He was astonished when he heard about this,” spokesman Andrew Wimer said. “He had worked on Kashmiri peace before he ever met this group. He has also remained critical of the Pakistani government throughout his time in Congress.”

The allegations have further strained tensions between the Obama administration and the government of Pakistan, which is angry about U.S. intelligence operations on its soil, including the May 2 raid that killed Osama bin Laden.

News of the case reverberated through Pakistan’s military and intelligence apparatus on Wednesday, where many suspect the timing of the charges was in retaliation for recent expulsions and arrests of Americans in Pakistan.

“It seems that some elements in Washington are against the normal ties . . . and whenever efforts are made to iron out the differences, then such sort of incident occurs,” said one Pakistani intelligence official who spoke on the condition of anonymity. He added that Pakistan would protest the accusations as “baseless propaganda.”

Federal prosecutors have charged two U.S. citizens in the case with failing to register as foreign agents: Syed Ghulam Nabi Fai of Fairfax, who is the Kashmiri council’s executive director, and Zaheer Ahmad, who lists his address as Brooklyn in disclosure records but is believed to be at large in Pakistan. Fai is jailed pending a hearing on Thursday.

Law enforcement officials said that more than a dozen warrants have been served in connection with the case this week, and that more charges are possible.

An FBI affidavit outlines a far-ranging effort by the ISI to set up a satellite of ostensibly pro-Kashmir groups to do its bidding, including similar organizations in London and Brussels. The Washington group, headed by Fai, was formed in 1990 and soon became well-known for its annual conferences on Kashmir and efforts to support friendly lawmakers with campaign contributions.

Fai and Ahmad themselves gave at least $30,000 in contributions to members of both parties, including Rep. Dan Burton (R-Ind.), a longtime pro-Pakistani lawmaker who was the largest single recipient, FEC records show. The two men also gave at least $4,500 to the National Republican Senatorial Committee, $4,000 to Pitts and $2,000 to Rep. James P. Moran (D-Va.), plus smaller donations to Barack Obama, Al Gore, Rep. Dennis J. Kucinich (D-Ohio) and others.

Most of the recipients have said they will return or donate the money to charity. Wimer said Pitts has given the $4,000 he received from the men to charities in Lancaster County, Pa.

But court and campaign records leave many questions unanswered, including precisely how much money may have been funneled to U.S. politicians by the ISI.

Financial records cited by the FBI suggest the Kashmir council budgeted up to $100,000 a year just for political contributions, many of which were allegedly dispersed through a network of pro-Pakistan advocates with U.S. residency or citizenship. So-called straw donors — who would be reimbursed by the ISI — were also used to fund the activities of the Kashmir council, according to the FBI affidavit.

Several of the council’s board members have given donations to Burton and other members of Congress, according to FEC and tax records. They did not respond to phone messages left at their homes or offices Wednesday.

In Islamabad, there was no official reaction from the Pakistani government or military, of which the ISI is a part. The chief military spokesman, Maj. Gen. Athar Abbas, referred questions to the foreign ministry, which did not respond to several calls. Abbas said he had no information about the military officials named in the FBI affidavit as Fai’s handlers over the years.

 “The retired people, really, are out of the establishment and they are on their own. For technical purposes, they are civilians,” Abbas said. Many top ISI figures are retired military officers.

 Mahmud Ali Durrani, a retired army major general who served as Pakistani ambassador to the United States from 2006 to 2008, said he was “taken aback” when he heard about the arrest of Fai, who he said was a familiar figure at the embassy and in Washington.

“He seemed a very mild, soft-spoken gentleman. He didn’t look like Mr. Spy Man,” Durrani said. Referring to the ISI, Durrani said: “I’m quite surprised. I didn’t know they would have such a long-standing, subtle campaign.”

Durrani said it was likely many in Pakistan would conclude that the charges are part of an Indian scheme to stifle discussions of Kashmiri independence. A prominent separatist leader in Indian-controlled Kashmir endorsed that idea on Wednesday, denouncing Fai’s arrest as India’s effort to rid the debate of someone it considered “an eyesore.” The separatist leader, Syed Ali Shah Geelani, called on Kashmiris to stage protests against the arrest on Friday.

Brulliard reported from Pakistan. Special correspondent Shaiq Hussain in Pakistan and staff researcher Lucy Shackelford in Washington contributed to this report.