A federal judge expressed concern yesterday that law enforcement officials were being “irrational” when they widened an investigation earlier this year into Warith Deen Umar, who was once the ranking Muslim chaplain for the New York state prison system.

The judge, Robert Patterson of U.S. District Court in Manhattan, said that before he sentenced Umar for illegal gun possession, he wanted to know more about the circumstances of the government’s searches of Umar’s home. Umar, 61, had been scheduled to be sentenced yesterday.

“We are going to make sure that he is not being harassed,”Judge Patterson said.

Governor Pataki and Senator Schumer had denounced Umar in 2003, after the Wall Street Journal quoted Umar as saying that all Muslims “secretly admire and applaud” the hijackers who perpetrated the September 11 terrorist attacks. Shortly after, Umar, already retired from the state chaplaincy, was barred from setting foot again inside the state prison system.

Yesterday, Judge Patterson expressed concern that prosecutors had left him in the dark about what had precipitated the case against Umar and the circumstances that had led state courts to issue search warrants of Umar’s home.

Judge Patterson pressed the federal prosecutor in the case, Jennifer Rodgers, to disclose what had tipped police off to Umar.

Judge Patterson brought up a “document accusing him of being a member of Al Qaeda,” and seemed to want to know where that fit into the case. The judge was apparently referring to a flyer circulating around Umar’s Bronx apartment building that called him a terrorist and urged tenants not to pay rent to Umar, whose wife owns the building.

“I want to make sure no irrational conduct is occurring in this case,” he said.

Outside the courtroom, Umar told reporters that he had “no idea” why he had become the subject of such intense police scrutiny in recent years.

But he suggested he was an easy target because of his writings and “radical poetry.” He said police, when they searched his home, had seen a copy of one of his poems.

Umar recalled one line: “I.E.D.’s will set you free,” he said, referring to improvised explosive devices that have been used with such lethality against troops in Iraq.

Asked what he meant by those words, Umar said, “This is the Iraqi in me speaking.” He said that he was a family man and was not dangerous.

He said that eight computers of his had been seized and that contraband-sniffing dogs had been through his home in Glenmont, New York. As a devout Muslim, he said he had been forced to throw away the carpets before his home was fit for prayer.

“Every citizen in America has a right to keep his papers,” Umar said. “You have a right to write what you want.”

Umar was scheduled to be sentenced for owning a rifle and a shotgun although he is a felon. The firearms, which Umar has owned for more than 20 years, came to the attention of law enforcement when Umar brought the shotgun out unloaded when he was threatened in his Bronx apartment building.

Yesterday, Judge Patterson had not yet ruled out that Umar was justified in wielding the unloaded shotgun.

“There are times,” Judge Patterson said, “when self-help is considered a reasonable thing to do.”

Ms. Rodgers, the prosecutor, acknowledged that Umar had been the subject of an intelligence investigation unrelated to the gun charges.