Dozens of grand jury subpoenas issued in a terrorism financing investigation of Muslim charities in northern Virginia have spawned a largely secret legal battle before a federal appeals court, according to court records and a person close to the investigation.

At least four appeals stemming from the inquiry are presently pending before the 4th Circuit in Richmond, but that court’s docket suggests that more than 30 subpoenas were challenged last year before the Alexandria, Va., district court where the grand jury was impaneled. One of the appeals involves a former Florida college professor, Sami Al-Arian, who pleaded guilty last year to a terrorism-support charge and is currently on a hunger strike to protest a judge’s order jailing him for refusing to testify before a Virginia-based grand jury.

Court records list Al-Arian’s case as related to the other subpoena fights. However, an attorney involved in the latter disputes, Nancy Luque, said this week that she knew of no particular connection. “None of it has directly to do with Al-Arian,” Ms. Luque said. She said she could not identify the entities involved in the appeals or discuss the grounds for them because they have been ordered sealed.

The flurry of subpoenas last year indicates that the investigation was more active in recent months than was previously known. Court filings indicate that the inquiry into terrorism financing and possible embargo violations began soon after the terrorist attacks of September 11, 2001. In March 2002, federal agents served search warrants at more than a dozen locations in northern Virginia, including a think tank, the International Institute for Islamic Thought. A similar operation Al-Arian ran in Florida, the World Islam & Studies Enterprise, received $55,000 from IIIT in the early 1990s, and an IIIT leader once described the two groups as intertwined.

The Virginia investigation has focused primarily on alleged links with the Palestinian Arab terrorist group Hamas, though the government has alleged that Al-Arian’s Florida operation was an arm of a rival terrorist organization, Palestinian Islamic Jihad.

In 2004, a prominent Muslim leader whose Virginia home was searched in the 2002 raids, Abdurahman Alamoudi, pleaded guilty to repeated violations of the trade embargo with Libya and admitted to involvement in a plot to kill Crown Prince Abdullah of Saudi Arabia. Alamoudi, who founded the American Muslim Council and once had entrée at the top levels of the Bush and Clinton administrations, was sentenced to 23 years in prison. In addition, an Egyptian banker, Soliman Biheiri, was convicted on immigration charges and a charge that he lied to investigators about his ties to a Hamas leader, Mousa abu Marzook. Biheiri got two sentences of about a year each and was released in 2005.

Since those cases concluded, however, there have been few signs of where the investigation is headed. The New York Sun has learned that one grand jury subpoena issued last year went to a Maryland-based group that espouses political and free-market reforms in the Islamic world, the Minaret of Freedom Institute. The group’s president, Imad-ad-Dean Ahmad, said immigration agents visited his home in November 2006, seeking notes about a panel discussion he moderated in 1999.

“They were looking for a seven-year-old event that was publicly broadcast on C-SPAN,” Mr. Ahmad told the Sun. The session, titled “The United States and Iran: It’s Time to Talk,” took place at the American Muslim Council’s annual conference in Crystal City, Va.

Mr. Ahmad said he was unsure why investigators were focused on that session, but said it could be because Al-Arian was there. “They showed me a list of attendees they had … I noticed Sami Al-Arian’s name was on the list,” Mr. Ahmad said. He added that the grand jury subpoena was signed by the same prosecutor who demanded Al-Arian’s testimony, Gordon Kromberg.

Another reason for prosecutors’ interest could be that the Minaret Web site says the panel was organized by a Springfield, Va. think tank, United Associates for Studies and Research. That operation was founded by Mr. abu Marzook, issued a forceful statement deploring Israel’s killing of a Hamas spiritual leader in 2004, and, according to the New York Times, was identified by a Palestinian Arab activist as Hamas’s American base of operations.

A former assistant secretary of state who spoke on the 1999 panel about rapprochement with Iran, Robert Pelletreau, told the Sun this week that investigators had not contacted him about the event. “It wouldn’t have been anything nefarious that there’d be a government interest in following up on,” he said.

Mr. Ahmad said he had no relevant notes and was ultimately excused from testifying to the grand jury. However, he said he suspects the subpoena was issued in retaliation for a July 2006 blog posting in which he criticized federal prosecutors in Virginia for using the Neutrality Act to charge 11 Muslims who used paintball guns as part of alleged practice for potential combat with India in Kashmir. “How many American citizens who violated the same law … by going to Israel to fight against Arab countries against whom the United States has not declared war have been prosecuted?” Mr. Ahmad asked on his site. He said the discrepancy was likely an indicator of “religious bias.”

Mr. Ahmad said he wrote to the U.S. attorney in Alexandria, Chuck Rosenberg, before raising the issue publicly last year and again last week. The Maryland activist said he has received no reply.

A spokesman for Mr. Rosenberg declined to comment yesterday about Mr. Ahmad’s letter. However, the prosecutor told the Washington Post last year: “We do not prosecute people because they are Muslims or Catholics or Jews. We prosecute them because they have committed criminal acts that warrant prosecution.” Last week, Mr. Rosenberg was named to replace the recently resigned chief of staff to Attorney General Alberto Gonzales.

Al-Arian’s attorneys also have complained of bias, alleging that the government lawyer directing the Virginia charities probe, Mr. Kromberg, exhibited an anti-Muslim attitude in rejecting Al-Arian’s request to delay his appearance until after Ramadan. “If they can kill each other during Ramadan, they can appear before the grand jury; all they can’t do is eat before sunset … I am not going to put off Dr. Al-Arian’s grand jury appearance just to assist in what is becoming the Islamization of America,” Mr. Kromberg said, according to a defense court filing.

Al-Arian, who pleaded guilty last year to one count of supporting a designated terrorist group, contends that prosecutors reneged on a promise that he would not have to testify before any grand jury. The former professor is appealing a judge’s ruling rejecting that argument.

Mr. Kromberg said earlier this year that grand jury secrecy rules preclude him from responding to Al-Arian’s claims of bias . The grand jury that subpoenaed Mr. Ahmad expired late last year, but another was convened recently to keep the five-year-old charities probe rolling.