Some human rights activists believe that Aafia Siddiqui, a Pakistani-born neuroscientist, who appeared on Tuesday in federal district court in New York, was originally “disappeared” by Pakistani authorities five years ago, possibly at US behest.

American officials said that Siddiqui had been arrested in Afghanistan last month and flown to the US on Monday after recuperating from a gunshot that authorities said she suffered in a shootout after her capture.

Siddiqui, who trained at the Massachusetts Institute of Technology, initially dropped out of sight in 2003 in Karachi, at a time when US authorities wanted to question her about her suspected ties to the al-Qaeda.

Human rights activists were divided over whether the Siddiqui case would ratchet up pressure on the 5-month-old Pakistani Government to account for the whereabouts of hundreds of people who have been reported missing by their families. Many presumed detainees are believed to be languishing incommunicado, denied access to counsel, but not charged with any crime.

“One hopes that this case is going to bring more attention to the issue of the ‘disappeared’, “ said Ali Dayan Hasan, Pakistan researcher for Human Rights Watch. His organisation and other rights groups had raised suspicion that Siddiqui was secretly held at some point by US or Pakistani authorities, or both.

The Pakistani Government has never acknowledged detaining Siddiqui and made no statement on Tuesday about her arrest. However, its diplomats in the US have sought consular access to her while she is in US custody, officials said.

Pakistan’s civilian Government has said it wants to move ahead with resolving missing-persons cases such as Siddiqui’s. But the governing coalition, beset by infighting, has had a difficult time establishing any significant authority over Pakistan’s intelligence establishment.

Most of the missing are thought to be held under the auspices of the military or security agencies such as the ISI.

Siddiqui’s lawyer in Pakistan, Iqbal Jaffry, has been trying to force officials to disclose any information they have about the neuroscientist’s whereabouts over the last five years.

The Pakistani Supreme Court agreed earlier to hear Jaffry’s motion, aimed at compelling the Government to disclose what it knows about Siddiqui’s status after her disappearance.