At the time of her arrest she was carrying documents on how to make explosives and descriptions of US landmarks in her handbag, according to the complaint against her in the court.
She was also carrying "chemical substances in gel and liquid form that were sealed in bottles and glass jars", the complaint said.
Siddiqui is also said to have fired on US military officials who arrived at her detention facility one day after her arrest, using an assault rifle one of them had placed on the floor.
An interpreter pushed the rifle aside as she fired two shots, which missed, the prosecution said. One of two shots fired by a soldier in response hit her in the torso and she was subdued.
Elaine Whitfield Sharp, a lawyer for Siddiqui's family, called the charges "a tall story" and disputed the US government's earlier claims that Siddiqui had gone underground for several years before her capture.
The family suspects that after she vanished with her three children while in Pakistan in 2003, she was secretly held and possibly tortured before US authorities finally brought charges to justify her detention.
"I believe she's become a terrible embarrassment to them, but she's not a terrorist," Sharp said. "When the truth comes out, people will see she did nothing wrong."
At the time of the incident, Afghan officials gave conflicting accounts of what transpired between Siddiqui and the US interrogators, while US officials offered no comment.
General Khan Mohammad Mujahid, police chief in central Ghazni province, initially said police argued with the Americans over giving up custody of Siddiqui, But he later said there was no argument and that the woman lunged at one of the US soldiers.
US authorities have said in the past that they believe Siddiqui, who received a biology degree from the Massachusetts Institute of Technology and wrote a doctoral thesis on neurological sciences at Brandeis University, outside Boston, has links to al-Qaeda.
Her arrest last month prompted protests in Pakistan, with demonstrators, many from Jamaat-i-Islami, calling for Siddiqui's release.
Siddiqui is charged with one count of attempting to kill US officers and employees, and one count of assaulting US officers and employees.
If convicted, she faces up to 20 years in prison on each charge.