Law enforcement officials familiar with the case said Friday that Medunjanin was facing more serious terror charges; one said he likely would be accused of seeking training from a terrorist organization. The officials were not authorized to discuss the case and spoke to The Associated Press on condition of anonymity.
During a brief appearance in federal court in Brooklyn, Ahmedzay was ordered held without bail until a hearing Tuesday. Defense attorney Michael Marinaccio noted that the indictment made no mention of terrorism.
"It seems to me that if (prosecutors) had that kind of information, we'd be reading about it in the indictment," he told reporters outside court.
Ahmedzay, 24, and Medunjanin, 25, were first publicly linked to the investigation in September, when investigators raided their homes shortly before the arrest of Najibullah Zazi, a Colorado airport shuttle driver who has pleaded not guilty to supporting terrorism. The former Queens high school classmates are suspected of going to Pakistan in 2008.
The latest arrests came after the FBI went to Medunjanin's Queens apartment Thursday afternoon with a search warrant and seized his passport. After the search, he apparently became upset and left in his car.
While driving erratically, Medunjanin called 911 and made angry comments referencing Allah, the law enforcement officials said. He got into an accident and was treated at a hospital for minor injuries.
Federal authorities later took him into custody for questioning before deciding to arrest him early Friday, the officials said. Agents arrested Ahmedzay at about 3 a.m. while he was driving a cab in the Greenwich Village area of Manhattan, authorities said.
"He's not guilty," Shried Ahmedzay, 22, his brother, said Friday. "He works hard to support his family."
The brother said it was obvious that authorities had him under surveillance for months, noting that unmarked cars frequently parked around his apartment building.
Medunjanin's attorney, Robert C. Gottlieb, has said FBI agents seized computers and cell phones from his client's apartment last fall but later returned them. He insisted Friday that Medunjanin had done nothing wrong and claimed that federal authorities hadn't let his client confer with him or his family since an arrest made "under incredibly suspicious circumstances."
Family members "have not been able to speak to him," he said. "They're frantic."
Prosecutors said that Zazi had recently traveled to al-Qaida training camp in Pakistan, and that "others" accompanied him on the trip to the country.
The indictment unsealed Friday accused Ahmedzay of lying during questioning in September about "all of the locations he visited during his trip to Pakistan and Afghanistan" in late 2008 and early 2009. It also alleged he lied about conversations with someone about "attending a camp to receive military-type training."
After receiving instruction on explosives, Zazi bought beauty supplies in a Denver suburb to make peroxide-based bombs, prosecutors said. He tried to mix explosives in a hotel room in early September, then drove to New York to carry out an attack, possibly on the transit system, they said.
Investigators secretly searched his rented vehicle in New York on Sept. 10 and found a laptop computer with bomb-making instructions, authorities said. Aware he was under surveillance, he flew back to Denver on Sept. 12 and was arrested a week later.
Authorities had said they believed other suspects were in on the plot. Two other men, including Zazi's father, have been charged with lying to the FBI, but no one else had been charged with terrorism.
Medunjanin, who is originally from Bosnia, and Ahmedzay, who was born in Afghanistan, are U.S. citizens. They and Zazi attended Flushing High School in Queens.
Medunjanin also played football at Flushing High and graduated in June from Queens College. Ahmedzay is licensed to drive a taxi in New York City and took the civil service exam to become a firefighter, although his score made him unlikely to get an appointment.
Barrett reported from Washington. Associated Press writers Kiley Armstrong, David B. Caruso and Marcus Franklin in New York contributed to this report.