Police and prison authorities denied any ill-treatment, and said the men did not bring up their complaints in court.
The allegations could add to political sensitivities surrounding the case, which comes amid growing anti-American sentiment in Pakistan.
Washington is also calling for the Muslim country to do more to fight al-Qaida and the Taliban.
The five, all Muslims, were detained in December after being arrested at the house of one of their relatives in the Punjabi town of Saragodha.
Police have publicly accused them of plotting terror attacks in Pakistan, having links to al-Qaida and seeking to join militants fighting U.S. troops across the border in Afghanistan. Lawyers for the men say they were focused only on Afghanistan.
In Monday's hearing, police submitted a charge sheet and evidence to the court in which the men are accused of violating several sections of Pakistan's penal code and anti-terrorism law. The most serious charge is conspiracy to carry out a terrorist act, which could carry life imprisonment depending on what the act is, according to prosecutor Nadim Akram Cheema and police officer Amir Shirazi.
The men were inside a prison van when several of them shouted in unison, "We are being tortured" three times within earshot of reporters. The media and the public were not allowed to attend the court session.
Aftab Haanif, the deputy superintendent of Sargodha jail where the men are being held, denied any kind of torture and said they were receiving better food than regular inmates.
A U.S. Embassy spokesman said he had no immediate comment, but said consular officials had visited the men.
The five men are between the ages of 19 and 25 and all from the Washington area. They were reported missing by their families in late November after one of them left behind a farewell video showing scenes of war and casualties and saying Muslims must be defended.
The next court hearing was set for early next month.