A doctor accused of playing a pivotal role in a plot to funnel cash from Pakistani intelligence into U.S. political campaigns is a respected figure in Pakistan who founded and runs one of the country’s leading hospitals, reporting by ProPublica shows.

The doctor, Zaheer Ahmad, 63, was charged Tuesday with conspiring to act as an unregistered agent of the government of Pakistan. In an affidavit filed in the case, an FBI agent alleges that Pakistani intelligence transferred money to Ahmad, who passed it through intermediaries to the Kashmiri American Council in Washington, a charity run by Syed Ghulam Nabi Fai. Fai, 62, who like Ahmad is a U.S. citizen, was arrested Tuesday in Virginia, where he lives. Authorities said Ahmad was believed to be in Pakistan.

A confidential witness quoted by the affidavit “said Ahmad told him he needed to get money to Fai in the United States, and that Fai would use it for the Kashmir cause and for lobbying.”

The money, at least $4 million since the mid-1990s, was allegedly spent on conferences and campaign donations aimed at swaying U.S. lawmakers on Kashmir, the disputed territory in India. It was provided by the Inter-Services Intelligence Directorate, or ISI, the U.S. government said. It’s not clear how much went to politicians; Fai wanted to spend about $100,000 on donations to Congress in 2008 alone, the affidavit said. It’s also not clear that any of the politicians had any idea where the money came from. The ISI is implicated separately in an ongoing U.S. investigation of the 2008 attacks in Mumbai.

A U.S. official speaking on condition of anonymity Wednesday confirmed that the man identified in court papers as Zaheer Ahmad is the same Zaheer Ahmad who runs the Shifa International Hospital in Islamabad. Ahmad could not be reached for comment on Wednesday evening.

Ahmad’s position in Pakistan highlights how difficult it will be to extradite him to the United States to face charges and, if the allegations in the affidavit are true, illustrates the ISI’s reach into the upper echelons of Pakistan’s elite. The charges are punishable by up to five years in prison.

The affidavit said that money from Pakistan was moved through a network of “straw donors” in the United States, comprised of U.S.-based Pakistani doctors and businessmen. These intermediaries donated small amounts to the council and were reimbursed, according to the affidavit by FBI agent Sarah Webb Linden. Four Pakistani men directed the operation for the government; Fai’s main handlers were two ISI officials, the affidavit said.

“I believe that Fai has received approximately $500,000 to $700,000 per year from the Government of Pakistan, and that the Government of Pakistan has funded Fai’s operations through Ahmad,” Linden wrote in the affidavit, before outlining how the government’s money was routed to Fai through Ahmad and a network of people connected to Ahmad. She also said she believed individuals in the United States helped Ahmad ostensibly to get tax deductions for donating to a charity.

The affidavit said Fai’s handlers communicated regularly with Ahmad, whose email account had contact information for Javeed Aziz Khan, allegedly the main ISI handler for Fai. When Ahmad arrived at JFK International Airport in New York on July 8, 2009, his PDA was examined, showing similar information, the affidavit said. Telephone records cited in the document show that Khan called Fai many times from the same phone number that Ahmad had for Khan. And both Khan and the other main ISI handler referred to Ahmad in conversations with Fai, calling him “the doctor” or “Zaheer,” the affidavit said.

At one point, in June 2008, Fai told Khan he needed “half a dozen Brylcreem,” or $60,000, and that it would be great to meet with “the doctor,” the affidavit said. Later, in August 2009, Khan emailed Fai that he “saw the doctor” and that his “consultation fee has increased by rupees 150,” thought to be code for a funding request Fai had earlier made for $150,000, the affidavit said.

Ahmad himself was credited with funneling about $367,700 to the council since 1993, according to receipts cited by the affidavit.

In the document, Linden wrote that “Elected Official A” reported getting a $2,000 donation from Ahmad on Sept. 13, 2004.

Campaign finance records show that Ahmad donated $2,000 to Rep. Joe Pitts, R-Pa., on Sept. 13, 2004. (Pitts was upset by the news Tuesday and donated the $2,000 from Ahmad and another $2,000 from Fai to charity, his office told the Lancaster Newspapers in Pennsylvania.)

The address for Ahmad in the campaign records is the same as one of the Brooklyn addresses for Dr. Zaheer Ahmad, who founded Shifa International Hospital in Islamabad after finishing his medical residency in the United States and moving back to Pakistan in 1985. Ahmad also is the chairman of the Tameer-e-Millat Foundation, founded in 1987 to help educate Pakistani children.

One Brooklyn doctor who knew Ahmad said he was not aware of the allegations but doubted that he could be connected to any case involving the ISI.

“I’ve known him many years,” said Dr. Tajammal Gilani, a Brooklyn doctor who’s listed as donating $350 to Pitts on the same day as Ahmad and Fai but said he did not remember the donation. “He’s an impressive person. He built a very good hospital.”

The case comes at a time of intense stress in the relationship between the United States and Pakistan. The FBI affidavit pulled no punches, repeatedly referring to the ISI and “the Government of Pakistan.” Earlier this month, U.S. officials publicly linked the ISI to the death of a Pakistani journalist and also moved to withhold $800 million in military assistance to Islamabad.

It’s unlikely Pakistan will extradite Ahmad, especially considering the charges of Pakistan's government involvement and his position. President Pervez Musharraf turned down a U.S. request in 2002 for the extradition of a man wanted in the murder of Wall Street Journal reporter Daniel Pearl. In December 2009, the Pakistani government denied having an extradition treaty. But weeks later, the government flip-flopped and said that there was one.