(Recasts with U.S. hearing, changes byline)
By Christine Kearney
NEW YORK, Aug 5 (Reuters) - A U.S. magistrate on Tuesday ordered a Pakistani woman suspected of high-level links to al Qaeda to be detained until next week on charges of trying to kill U.S. soldiers in Afghanistan.
Aafia Siddiqui, 36, was charged with attempted murder and assault and will reappear in federal district court in Manhattan on Monday for a bail hearing. She did not enter a plea, but her lawyers argued the mother of three, who they said weighed 90 pounds (41 kilograms), was innocent.
"There is a physical discrepancy between this really fragile woman and what has been alleged," defense lawyer Elaine Sharp said after the hearing. She denied that Siddiqui had links to al Qaeda.
A neuroscientist trained at the Massachusetts Institute of Technology and Brandeis University, Siddiqui was flown to New York on Monday. Pakistan's ambassador to Washington has sought consular access to her.
Siddiqui was shot and wounded last month while allegedly trying to fire on a group of U.S. troops who had come to question her in Afghanistan's Ghazni province.
In 2004, Siddiqui was identified by the FBI as an "al Qaeda operative and facilitator who posed a clear and present danger to America."
She was married to a nephew of Khalid Sheik Mohammed, who helped plan the Sept. 11 attacks. Her husband was captured in 2003 and is currently held at the Guantanamo Bay prison.
Wearing maroon headscarf and black pants, Siddiqui answered questions from the judge in a soft voice. She shook her head as the two charges were read.
Accounts of Siddiqui's arrest and the shooting incident differed between U.S. prosecutors and Afghan police.
The Justice Department said she was arrested outside the governor's office in Afghanistan's Ghazni province on July 17 after police searched her handbag and found documents on making explosives, excerpts from the book "Anarchist's Arsenal" and descriptions of New York City landmarks.
While detained in a meeting room, Siddiqui grabbed the M-4 assault rifle from a U.S. Army warrant officer who had placed the weapon on the floor, the statement said. Two FBI agents were also in the room.
Siddiqui fired at least twice at the captain but the shots missed as a military interpreter lunged at her. The warrant officer then shot her with his pistol, the statement said.
"Despite being shot, Siddiqui struggled with the officers when they tried to subdue her; she struck and kicked them while shouting in English that she wanted to kill Americans," the statement added. She then lost consciousness and was treated.
Afghan police in Ghazni told a different story. They said officers searched Siddiqui after reports she was behaving suspiciously and found maps of Ghazni, including one of the governor's house. They arrested her along with a teenage boy.
U.S. troops requested the woman be handed over to them but the police refused, a senior Ghazni police officer said.
U.S. soldiers then disarmed the Afghan police, at which point Siddiqui approached the Americans complaining of mistreatment by the police, the officer said.
The U.S. troops, the officer said, "thinking that she had explosives and would attack them as a suicide bomber, shot her and took her." The boy remained in police custody.
Siddiqui and her three children disappeared from her parents' home in the port city of Karachi in 2003 and Pakistani human rights groups had said they believed she had been held at Bagram, the main U.S. base in Afghanistan.
Siddiqui's lawyers had repeatedly claimed she had been secretly detained since March 2003, when she left her parents' home to visit her uncle in Islamabad. They also said she does not know where her children are.
U.S. officials believe Siddiqui was in Pakistan until her arrest in neighboring Afghanistan, the New York Times said.
Family members said Siddiqui was raped and tortured at Bagram, although they did not say how they knew this.
The Human Rights Commission of Pakistan demanded the Pakistani government intervene and secure her release.
"Dr. Aafia's case is a reminder of the grave injustice done to God knows how many Pakistanis in U.S. detention facilities in Bagram in Afghanistan, Guantanamo Bay and elsewhere, who have been listed as missing," it said in a statement. (Additional reporting by Aftab Borka and Imtiaz Shah in Karachi and Sher Ahmad in Ghazni; Writing by Daniel Trotta, Michelle Nichols and Jon Hemming; Editing by Alan Elsner)