In a scathing attack on the Pervez Musharraf government, human rights body Amnesty International has alleged that Baloch and Sindhi nationalists are among activists who have become victims of "enforced disappearance" in the country.
Among other cases being reported, it said that now cases of enforced disappearance of Baloch and Sindhi nationalists were now being reported.
This was part of what it called "news patterns of enforced disappearance" related to the war on terror.
In a press release on the International Day of the Disappeared, Amnesty believed that several hundreds of people had become victims of enforced disappearances in Pakistan in the context of the "war on terror".
Amnesty said: "Whilst many of those have eventually been acknowledged as being held in Guantanamo Bay, others are believed still to be held in Pakistani detention although their precise whereabouts remain unknown.
"Some people were released after receiving threats not to reveal details about their detention, while others were subsequently criminally charged.
In at least one case, the body of a victim of enforced disappearance was found six months after he had been captured. The fate or whereabouts of many others remain unknown."
"South Asia has a history of enforced disappearances, with tens of thousands of people going missing over past decades in countries such as Nepal and Sri Lanka.
It is very disappointing to see countries such as Pakistan join in a trend that one would hope would be declining," said Catherine Baber, Deputy Asia Pacific Director at Amnesty International.
She added: "Enforced disappearance is a gross violation of international human rights and humanitarian law. It affects not only the victims but also takes a heavy toll on their families.
Relatives are left to agonise over the fate of their loved ones in the face of official denials and contradictions.
They are harassed in their attempts to obtain information and face financial difficulties when the victim is the breadwinner."
In Pakistan, Amnesty said that the indifference shown to the enforced disappearance of terror suspects had contributed to its spread beyond "war on terror" related cases.
Courts were reportedly swamped with habeas corpus petitions to determine victims' whereabouts. State agents routinely denied holding the victims or knowing anything about their fate or whereabouts, it added.
"People should be arrested and detained according to the law, not forced into a van in the middle of the night and swept off to an anonymous detention centre where they risk torture and further abuses.
Individuals have the right to challenge their detention, to see a lawyer of their choosing and talk to their families. Families have a right to know where their relatives are," said Baber.