(CNN) -- A federal magistrate set bail at $50,000 Monday for one of the three men charged with lying to federal agents during a wide-ranging terrorism inquiry, as the men made their first appearances in courtrooms in New York and Colorado.
Najibullah Zazi is accused of making false statements to officials about an alleged bomb plot in the United States.
Mohammed Wali Zazi, 53, whose son is at the center of the terrorism investigation, will be allowed to go home under electronic monitoring and required to remain there except for work, medical care, religious services or court appearances, prosecutors said.
U.S. Magistrate Judge Craig Shaffer in Denver, Colorado, set bail at $50,000, but Zazi is unlikely to be released until later this week.
Prosecutors are asking that his son, 24-year-old Najibullah Zazi, be held until trial. Shaffer set a detention hearing for the younger Zazi for Thursday.
Investigators said Najibullah Zazi has admitted attending courses and receiving instructions on weapons and explosives at an al Qaeda training facility in Pakistan's tribal areas during a 2008 trip and lied to federal agents about explosives-handling instructions they found on his computer.
His attorney, Arthur Folsom, has denied the allegations.
The Zazis and Ahmad Wais Afzali, a 37-year-old Muslim cleric and funeral director from the New York borough of Queens, are the first people charged in connection with what the Justice Department has said was a plot to detonate bombs in the United States.
Earlier Monday, Afzali appeared in a federal court in New York, where a not-guilty plea was entered on his behalf. He smiled as he listened to the magistrate read the charge against him, blowing kisses to his wife during the hearing.
Ron Kuby, Afzali's lawyer, said his client had tried to help federal agents find Najibullah Zazi and called the charge against his client "a bootstrap case" the government brought "to cover up their own failings and the fact that they were the ones who blew this investigation."
According to affidavits outlining the charges against him, Afzali warned Najibullah Zazi that his phone call was being monitored. But Kuby said Afzali was helping "absolutely frantic" federal agents find Zazi, who had attended his Queens mosque with his family as a teenager.
"My client didn't tip him off, he was already tipped off," Kuby said. "And now the FBI is looking for somebody to blame."
Afzali was ordered to remain in custody until a bond hearing later this week. Kuby said his client had been an occasional source for New York's Joint Terrorism Task Force when it looked into previous terror plots, and a detective who had sought out Afzali as a source in previous cases would testify on the imam's behalf Thursday.
All three suspects are originally from Afghanistan. Mohammed Wali Zazi is a naturalized U.S. citizen, and Afzali and Najibullah Zazi are permanent legal residents. If convicted, each faces eight years in prison. Watch why authorities wanted to talk with Zazi »
The plot may have been targeting a major transportation center, such as a large railroad or subway station, sources close to the investigation said last week.
Federal agents have "no specific information regarding the timing, location or target of any planned attack," David Kris, assistant attorney general for national security, said in a written statement.
Court papers describe conversations among the men. At one point, according to the papers, Afzali warned Najibullah Zazi that their phone call was being monitored.
"I was exposed to something yesterday from the authorities," Afzali allegedly told Zazi in a September 11 call. "And they came to ask me about your characters. They asked me about you guys. ... I told them that they are innocent, law-abiding."
Afzali, however, called the questions from police "a good sign."
"The bad sign is for them coming to you guys and picking you up automatically," he said. And he allegedly told the younger Zazi, "Don't get into the Afghanistan garbage, Iraq garbage. ... Listen, our phone call is being monitored."
The federal complaint against Afzali says he falsely asserted that he never told Zazi that agents were monitoring him on the phone, an assertion Kuby slammed.
"Why on Earth is the imam going to lie to the FBI about the contents of a conversation that he knows they're recording?" Kuby asked Monday.
The criminal complaint against Afzali also says he falsely told federal agents that he did not ask Zazi about evidence in his rental car.
The inquiry emerged after a series of raids in Queens on September 14, three days after the intercepted calls. A police stop of Najibullah Zazi during a visit to New York raised investigators' concern that he would discover he was under surveillance, a former counterterrorism official familiar with the investigation said last week.
At the Queens residence where Zazi stayed during his visit, FBI agents seized a black scale containing several AA batteries. Zazi's fingerprints were on both, the criminal complaint against him said.
And agents searched his rental car and laptop computer while he was there, turning up what they said were handwritten notes of his that explained how to make, handle and detonate explosives, according to the complaint.
An FBI expert determined that the handwriting in the photographed document was similar to Najibullah Zazi's, according to the complaint. But during an interview with investigators Wednesday, Zazi denied having the instructions and said that if it was found on his computer, he must have unintentionally downloaded it as part of a religious book. He said he deleted the book within days after he realized that its contents discussed a holy war, investigators said.
According to court records, Mohammed Wali Zazi falsely told investigators that he had not called, nor had he received a call, from anyone in New York asking him about his son's activities. He also said he did not know anyone named Afzali, despite recorded phone calls that showed he did, the FBI stated.
CNN's Jeanne Meserve, Jim Spellman and Deborah Feyerick contributed to this report.