The international "war on terror" has led to new patterns of disappearances in South Asia, human rights group Amnesty International says.
Pakistani troops are on the front line in the "war on terror"
Hundreds of suspects had been removed without explanation in Pakistan, the group said in a report on Wednesday.
Fears were also voiced over Sri Lanka and Nepal, echoed by the UN, where civil wars have taken their toll.
The Amnesty report and the UN appeal were timed to coincide with the International Day of the Disappeared.
"South Asia has a history of enforced disappearances, with tens of thousands going missing over the past decade in countries such as Sri Lanka and Nepal," says Catherine Baber of Amnesty International.
"It is very disappointing to see countries such as Pakistan join in a trend that one hoped would be declining."
In Pakistan, the human rights group says many of those who disappeared have eventually been acknowledged as being held in Guantanamo Bay.
But the report, released on Wednesday, adds: "Others are believed still to be held in Pakistani detention although their precise whereabouts remain unknown."
Pakistan's Foreign Ministry spokeswoman, Tasnim Aslam, told the Associated Press news agency that the authorities were responding to the threat of terrorism.
"We have a problem of terrorism and obviously in most cases you can't wait for something to happen," she said.
"On the basis of information or suspicions, people are detained for investigations. When you try to balance between the need to fight and prevent terrorism and personal freedoms there is a challenge there for everybody, not only Pakistan."
Ms Aslam said she was unaware of individual cases of people disappearing but would study the Amnesty report for any cited cases to be followed up.
Impact on families
In Sri Lanka, the report says, there is a new pattern of state agents seizing opponents, after new emergency regulations gave security forces sweeping powers a year ago.
Over the past year, 62 cases of enforced disappearances have been registered in the north of the country alone by the Human Rights Commission of Sri Lanka.
The commission is investigating another 183 disappearances, says the report.
"Relatives are left to agonise over the fate of their loved ones in the face of official denials and contradictions," the report says.
The report also expresses concern over people missing in Nepal and in Indian-administered Kashmir.
In Nepal, it says a government committee announced in July that it was investigating more than 600 cases of enforced disappearances, but local activists say more than 1,000 individuals remain unaccounted for.
The United Nations added its voice on Nepal, urging political players to establish accountability for the fate of hundreds who disappeared in the course of the decade-long conflict there.
In Jammu and Kashmir, an estimated 8,000-10,000 enforced disappearances have been reported since 1989.
Amnesty's report says "while fewer new cases are reported now, there is still no information about past cases".