The nation’s preeminent civil liberties group is accusing the University of maintaining a political intelligence unit within the Harvard University Police Department (HUPD), an allegation that comes after two protesters were arrested during a demonstration in the Square.

The protesters allege that undercover HUPD officers were photographing the demonstration, according to John Reinstein, the legal director of the Massachusetts division of the American Civil Liberties Union (ACLU).

“What we found really quite surprising and disturbing is that the Harvard police department has an undercover, plainclothes, political intelligence unit which so far as I know has never been acknowledged by them before,” Reinstein said.

HUPD spokesman Steven G. Catalano declined to comment, and a University spokesman did not comment as well.

The protesters, Patrick Keaney and Lisa Nieves, were arrested March 3 in front of the Holyoke Center according to the HUPD’s police log. The log said that “officers were monitoring a demonstration” prior to the arrest.

“Two demonstrators became confrontational and acting in an aggressive manner toward one of officers,” the log said.

Keaney was charged with resisting arrest and Nieves was charged with disturbing the peace. The charges against Nieves have since been dropped, though Keaney’s case is still pending in the Cambridge District Court, according to Reinstein.

Reinstein said that the ACLU has filed a request under the Freedom of Information Act to discover whether Harvard shares the intelligence it gathers with the federal government. Other schools have connections with the FBI’s Joint Terrorism Task Forces (JTTFs), local teams of law enforcement and intelligence specialists formed to investigate terrorism.

According to the FBI’s Web site, there are JTTFs in 100 cities across the U.S., including one in Boston.

Shareef Fam, a member of the Boston Coalition for Palestinian Rights who was at the protest, said that the protest was nonviolent and that he spoke with uniformed police officers about keeping pedestrian passageways clear at the beginning of the event. He said that Nieves was taking pictures during the protest, which was called by Harvard students, with the intent of distributing the photos later to the rest of the protesters present.

Reinstein said that Nieves noticed a bystander in plainclothes taking photos of the protest and decided to go photograph him. When she did, the man informed her that he was an undercover police officer with HUPD and placed her under arrest for refusing to delete the photos. Kearney said that the officer would have to arrest him if he was going to arrest Nieves and so Kearney was also arrested, according to both Fam and Reinstein.

“It’s a little unnerving to find Harvard undercover police spying and taking pictures of Harvard students on public property,” Fam said.

—Staff writer Jamison A. Hill can be reached at jahill@fas.harvard.edu.