The house in Sargodha was raided after a period of surveillance
Five US citizens being held in Pakistan on suspicion of plotting attacks in Pakistan and Afghanistan say they have been tortured in custody.
They made the allegations in comments shouted to reporters as they were being driven from court in eastern Pakistan.
Authorities deny the charge, saying the men made no such complaint in court.
The five students were arrested in a raid in the city of Sargodha in December and face lengthy jail terms if found guilty. They deny any wrongdoing.
The Americans were inside a prison van when several of them shouted "we are being tortured" within earshot of reporters, the Associated Press news agency reported.
Aftab Haanif, the deputy superintendent of Sargodha jail where the men are being held, denied there had been any torture and said the defendants were receiving better food than regular inmates, the agency reported.
Police also dismissed the accusation.
"None of the five men said anything of the sort in the court. As far as I know, one of these men had a stomach problem," one officer told the AFP news agency.
The media and the public were not allowed to attend Monday's hearing, at which the men were remanded in custody until 2 February. Police said they had submitted an interrogation report running to about 250 pages.
The next hearing was set for 2 February.
At the first remand hearing, on 4 January, police said they planned to press for life sentences for the men.
'Contacts with militants'
The five young Muslims disappeared from the US state of Virginia in November.
Their families reported them missing after finding a farewell video message, which is said to have shown scenes of war and calls for Muslims to be defended.
Two of them are Pakistani-Americans, while the remaining three are of Eritrean, Ethiopian and Egyptian origin, officials said. All of them have US passports.
Police said laptops, mobile phones and maps of Pakistani cities were recovered from the property during the operation.
They said the men had been in direct contact with various militant groups in Pakistan since August.