The three were arrested early Tuesday after officers on patrol spotted the burning flag and tore it from the pole where it was mounted to the house on Chapel Street, police said.
Said Hyder Akbar, 23, Nikolaos Angelopoulos, 19, and Farhad Anklesaria, also 19, were arrested.
Marc Suraci, 37, owner of the two-story house on Chapel Street where the flag was burned, said he always puts flags out in front of his rental properties and said several of his relatives fought in American wars to defend the constitutional right to burn the flag as a protest.
"It makes me sick to my stomach to think that someone would burn the American flag," Suraci, who believes flag burning should be illegal, told the New Haven Register. "But it gets to another level when it is somebody else's flag on their own personal property."
Freshmen Angelopoulos and Anklesaria are both foreign citizens; Anklesaria is British and Angelopoulos is Greek. Akbar, a senior, was born in Pakistan, according to police, but is a U.S. citizen. Both Anklesaria and Angelopoulos had to turn over their passports.
Akbar worked as an informal translator for U.S. forces during the invasion of Afghanistan and later published a memoir, "Come Back to Afghanistan," based on his experiences there, the Yale Daily News reported Wednesday.
"He's an incredibly articulate, mature, sweet, smart guy," said Gillian Blake, Akbar's editor. "It's an amazing book."
Akbar — whose father was a spokesman for the Afghan president and served as governor — also testified at the trial of David Passaro, a former CIA contractor charged in the death of an Afghan citizen in U.S. custody.
Akbar said in 2004 he walked out of the interrogation in disgust after the contractor began threatening the prisoner, but that he said he saw no abuse. He testified that Passaro was "full of rage" during the interrogation.
Passaro, a former Hartford police officer, was the first American civilian charged with mistreating a detainee during the wars prompted by the Sept. 11 attacks.
He was sentenced in February to nearly 8 1/2 years in prison for beating a man in Afghanistan who later died.
At their arraignment in Superior Court a few hours after their arrests Tuesday, bond was kept at $25,000 for Angelopoulos and Akbar, but was reduced to $15,000 for Anklesaria.
The students appeared dazed at their arraignment Tuesday morning when they entered Superior Court in leg irons and handcuffs, reported The New Haven Register. They remained jailed Tuesday night but were later released on bond.
None have criminal records, Deputy Assistant Public Defender Sanford Bruce Wednesday.
"All three of these gentlemen are clearly happy to be in the United States and happy to be attending Yale," Bruce said.
He declined to discuss a possible motive for the alleged incident, but he challenged the arson charge.
The three are being charged with two counts of reckless endangerment, breach of peace, criminal mischief in the third-degree, arson in the second-degree, conspiracy for arson, conspiracy for breach of peace, conspiracy for mischief and conspiracy for reckless endangerment. They were not charged with flag burning.
Some charges were added by Assistant State's Attorney Karen Roberg after the three were arrested and charged by New Haven police. She substituted the arson charges for reckless burning.
Police said the students had two encounters with officers.
Officers Stephanija Van Wilgen and Diane Gonzalez were responding to an unrelated call in New Haven at about 3 a.m. and were flagged down by the students, who asked for directions.
A short time later, the two officers returned to Chapel Street to see if the students had found their way home and spotted the burning flag.
"There was a glow in front of the house which they identified as a flag mounted on a pole to the house and it was engulfed in flames," police spokeswoman Bonnie Posick said.
Van Wilgen pulled down the burning flag to prevent the fire from spreading, and Gonzalez tracked down the young men.
"People could have been hurt," Posick said, noting the flag was attached to the house. "They even admitted it was a stupid thing to do."
The police report says one of the officers woke up the residents on the first and second floors of the house to tell them about the incident. The people living there are not the homeowners, however, and likely are renters.
The police report does not indicate whether or not alcohol was involved in the incident, but the students were not given sobriety tests.
The Associated Press contributed to this report.