Investigators said they found notes on bomb-making instructions that appear to match Zazi's handwriting on his laptop, and discovered his fingerprints on materials - batteries and a scale - that could be used to make explosives.
Publicly, law enforcement officials have repeatedly said they are unaware of a specific time or target for any possible attacks. Privately, officials speaking on condition of anonymity because they weren't authorized to discuss the case said investigators have worried most about the possible use of backpack bombs on New York City mass transit trains, similar to attacks carried out in London and Madrid.
Backpacks and cell phones were taken from apartments in the Queens raids last week.
A joint FBI-New York Police Department task force feared Zazi may have been involved in a potential plot involving hydrogen peroxide-based explosives like those cited in an intelligence warning issued last week, according to two law enforcement officials, who spoke on condition of anonymity because they were not authorized to speak about the investigation.
On Monday, federal officials reminded law enforcement across the country that rail and transit systems can be vulnerable to terrorist attacks.
In a joint assessment, the FBI and Homeland Security Department warned that improvised explosive devices are the most common tactic to blow up mass transit and rail systems overseas. And they noted incidents where homemade bombs were made with various types of peroxide.
In the assessment, obtained by The Associated Press, officials recommended that transit system security officials conduct random sweeps at terminals and stations and that law enforcement make random patrols and board some trains and buses.
Zazi and his 53-year-old father, Mohammed, were arrested Saturday in Denver. An associate, Ahmad Wais Afzali, 37, was arrested in New York, where he is an imam at a mosque in Queens.
All face the same charge of lying to the government in a matter involving terrorism. If convicted, they face eight years in prison.
Mohammed Zazi and Afzali are accused of lying to FBI agents about calls between Denver and New York. An affidavit accuses Afzali of lying about a call in which he told Najibullah Zazi that he had spoken with authorities.
Zazi's father is accused of lying when he told authorities he didn't know anyone by the name of Afzali. The FBI said it recorded a conversation between Mohammed Zazi and Afzali.
Najibullah Zazi, in the same shirt, jeans and tennis shoes he wore when he was arrested, spoke little during the court hearing Monday except to say, "Yes," when asked if he understood the charge against him.
Mohammed Zazi asked to be represented by a federal public defender. He was expected to be released within 48 hours, after authorities determine whether he can be electronically monitored from his home.
Afzali appeared in federal court Monday in Brooklyn and was ordered held without bail. His attorney, Ron Kuby, said he would seek bail Thursday.
The younger Zazi has publicly denied being involved in a terror plot. His attorney, Arthur Folsom, dismissed as "rumor" any notion that his client played a crucial role.
Carl Tobias, a University of Richmond law professor who tracks such investigations, said authorities could have made the arrests because they feared too much information was getting to the suspects. Additional charges could be filed later, he said.
Kuby has said the government may have been forced to act after Najibullah Zazi went to New York. Zazi has said he drove there in September to resolve issues with a coffee cart he owns in Manhattan.
Kuby said Monday that his client had fully cooperated with the FBI, and was aware all along that his phone calls were being monitored.
"Why in the world is he going to lie about the content of a conversation that he knew was being taped?" Kuby said before Afzali's court appearance.
He accused authorities of trying to make Afzali a scapegoat for a botched investigation.
"The government wants somebody to blame for the fact that they haven't caught any terrorists," he said.
An arrest warrant affidavit alleges Zazi admitted to FBI agents that he received instruction from al-Qaida operatives on subjects such as weapons and explosives. It also says he received the training in the federally administered tribal areas of Pakistan.
The FBI said it found images of handwritten notes on a laptop containing formulas and instructions for making a bomb, detonators and a fuse. Zazi told the FBI that he must have unintentionally downloaded the notes as part of a religious book and that he deleted the book "after realizing that its contents discussed jihad."
An affidavit says the handwriting on the notes appeared to be Zazi's. It also says they were e-mailed in December as an attachment between accounts believed to be owned by Zazi, including an account that originated in Pakistan.
FBI agents say Najibullah Zazi traveled to Pakistan twice this year. Zazi says he was visiting his wife, who lives in the Peshawar region.
Zazi was born in Afghanistan, moved to Pakistan at age 7 and emigrated to the United States in 1999. He returned to Pakistan in 2007 and 2008 to visit his wife, according to Folsom.
Aaron Donovan, spokesman for the Metropolitan Transportation Authority, said the MTA was in touch with the New York City area's joint terrorism task force, but wouldn't comment Monday on any communications it had received from the NYPD or FBI. The agency operates the city's subways - carrying about 8 million daily riders - and commuter rail lines.
Associated Press writers Eileen Sullivan and Devlin Barrett in Washington, D.C., Ivan Moreno in Denver, and Samantha Gross, Jennifer Peltz and Larry Neumeister in New York City contributed to this report.