Pakistan's military and intelligence agencies, apparently trying to avoid acknowledging an elaborate secret detention system, have quietly set free nearly 100 men suspected of links to terrorism, few of whom were charged, human rights groups and lawyers say.

Those released, they say, are some of the nearly 500 Pakistanis presumed to have disappeared into the hands of the Pakistani intelligence agencies cooperating with the United States' fight against terrorism since 2001.

No official reason has been given for the releases, but as pressure has mounted to bring the cases into the courts, the government has decided to jettison some suspects and thereby spare itself the embarrassment of having to reveal that people have been held on flimsy evidence in the secret system, its opponents say.

Interviews with lawyers and human rights officials and a review of cases and court records by the New York Times show how scraps of information have accumulated over recent months into a body of evidence of the detention system.

In at least two other instances, detainees were handed over to the United States without any legal extradition proceedings, Pakistani lawyers and human rights groups say. U.S. officials here and in Washington refused to comment on the cases.

"They are releasing them because these cases are being made public," said Shaukat Aziz Siddiqui, a lawyer working at the Supreme Court who has taken up many of the cases of the missing. "They want to avoid the publicity."

In addition, human rights groups and lawyers contend, the government has swept up at least 4,000 other Pakistanis, most Baluchi and Sindhi nationalists campaigning for ethnic or regional autonomy who have nothing to do with the U.S. campaign against terrorism.

In total, human rights groups and lawyers describe the disappearances as one of the grimmest aspects of Pervez Musharraf's presidency, and one that shows no sign of slowing.

Under previous governments, "there were one or two cases, but not the systematic disappearances by the intelligence agencies under Musharraf," said Iqbal Haider, secretary-general of the Human Rights Commission of Pakistan, an independent nonprofit organization.

The Pakistani government denies detaining people illegally and says that many of the missing are actually in regular jails on criminal charges, while other cases have been fabricated.

The issue of the missing became one of the most contentious between Musharraf and the Supreme Court under its former chief justice, Iftikhar Mohammed Chaudhry.

The releases are particularly galling to lawyers because as one justification for imposing emergency rule on Nov. 3, Musharraf accused the courts of freeing terrorism suspects. That decree was lifted Saturday, but the former chief justice and other judges were dismissed and remain in detention. The Supreme Court hearings on the missing have been halted.

While Musharraf criticized the court as being soft on terrorists, court records show that Chaudhry was less interested in releasing terrorism suspects than in making sure their cases entered the court system.

He said at each hearing that his primary concern was for the families of the missing, who were suffering great anguish not knowing where their loved ones were.

His main aim was to regularize the detention of the missing, not to free them, Siddiqui said. "Not a single person who was convicted was released on the Supreme Court's order," he said.

Detainees have been warned on their release not to speak to anyone about their detention, yet fragments of their experiences have filtered out through relatives and their lawyers. A few even appeared in court and told their stories, and it became increasingly clear that the "disappeared" men had in fact been held in military or intelligence agency cells around the country, often for several years without being charged.

Still, the government denies detaining people illegally or torturing them. Brig. Javed Iqbal Cheema, a spokesman for the Ministry of Interior and leader of the national crisis management cell that deals with terrorism, said many of the men said to be missing had been found in jails or police cells and had been charged with crimes.

Others, he said, may have gone to the hills or Afghanistan to fight and died there. Still others, he suggested, were fabricated. "Let me assure you that there's a lot of politics going on into the missing persons also," he said.

Critics say that abuses continue. The director of the human rights commission, I.A. Rehman, said the government had set up a nearly invisible detention system. "There are safe houses in Islamabad where people are kept," he said, citing accounts from the police and those who have been freed. "Police have admitted this, flats are taken on rent, property is seized, people are tortured there."

In some cases, detainees recounted that they had been interrogated in the presence of English-speaking foreigners, who human rights officials and lawyers suspect are Americans.

A U.S. Embassy spokeswoman said she could not comment on the allegations and referred all questions to Washington. A spokesman for the CIA, Mark Mansfield, declined to comment on Rehman's accusations, or on any specific detainees.

One detainee, a Jordanian named Marwan Ibrahim, who was arrested in a raid in Lahore, where he had been living for 10 years, said he was sent to a detention center in Afghanistan run by Americans, then to Jordan and Israel, and was finally released in Gaza, according to an account Ibrahim gave to Human Rights Watch, another independent group.

Another detainee, Majid Khan, 27, a Pakistani computer engineer who disappeared from Karachi four years ago, surfaced April 15 this year before a military tribunal in Guantanamo Bay, Cuba. His American lawyers say he was subjected to torture in CIA detention in a secret location. Mansfield, the CIA spokesman, declined to comment, except to say that the "CIA's terrorist interrogation effort has always been small, carefully run, lawful and highly productive."

"Fewer than 100 hardened terrorists have gone through the program since it began in 2002," he said, "and, of those, less than a third required any enhanced interrogation measures."

As more and more such accounts have come to light, Musharraf has fought vigorously to keep the details of Pakistan's secret detentions hidden.

A week into emergency rule, he passed a decree amending the 1952 Army Act to allow civilians to be tried by military tribunals for general offenses. The tribunals are closed to the public and offer no right of appeal.

The amendment was made retroactive to January 2003. Haider of the human rights commission said the amendment was to cover the illegal detentions by the intelligence agencies. "These agencies have gone berserk, and Musharraf is legitimizing their acts," he said.

Cheema, the Interior Ministry spokesman, acknowledged that prosecutors and investigators had had difficulty pinning crimes on detainees. Hundreds of people in Guantanamo have not been charged either, he pointed out. The Army Act amendment would resolve much of the problem, he said.

"Sometimes it becomes difficult to prove a case, but you have reasons that a person poses a threat to humanity and to society," he said.

The intervention of the Supreme Court under Chaudhry was undoubtedly exposing this system of secret detentions.

He first took up the cases of the missing in 2006, demanding that the government trace the detainees and account for them.

His steady requests for information from senior police, Interior Ministry and military officials in court helped to trace nearly 100 detainees. Most of those were subsequently released without charges.

"This was very embarrassing to the government because the people who were supposed to be found and released, they told all their stories," said Rehman, the director of the human rights commission.

Amina Masood Janjua, who has led a campaign to trace the missing, first learned about news of her husband, who disappeared in July 2005, from a written account by another detainee. Later the detainee, Imran Munir, was produced in court and told her he had been held in the military base at Chaklala, in Rawalpindi, and saw her husband in another cell.

Another detainee, Hafiz Muhammad Tahir, was brought before the court and told the judges he had been ordered by the police to give a false account of his detention and charges against him, Janjua said. In fact he had been held secretly for three years without charge. The chief justice ordered him to be freed, and he was released the same day.

But only four or five detainees ever appeared before the Supreme Court. The majority of the 100 detainees released this year have been freed surreptitiously by the police and intelligence agencies, lawyers and human rights officials said.

"They cannot admit that they had these people because they have no charges against them, no documentation," Janjua said.