The revelations come from unidentified guards at the US military base, intelligence agents and others who worked in the prison who talked to the daily.
US military officials have long maintained such treatment had occurred in isolated cases only.
Prisoners at the Cuban base include those captured in Afghanistan and Iraq and suspected of association with or membership in what are termed "extremist" organisations.
Human-rights groups have criticised the United States for indefinitely detaining prisoners at the base, most without charges or legal representation.
Earlier this year, photographs of US personnel abusing Iraqi prisoners at Abu Ghraib prison outside Baghdad generated outrage around the world.
The Times reported in its Sunday editions that prisoners at Guantanamo deemed uncooperative were stripped to their underwear, shackled hand and foot to a bolt in the floor, and forced to endure strobe lights and loud music played from close loudspeakers.
At the same time, the air-conditioning was turned up to maximum levels for periods as long as 14 hours.
The treatment was described to the newspaper by a military official who said he witnessed the procedure and others who said they participated in the techniques, all of whom spoke on condition of anonymity.
"It fried them," the newspaper quoted the official as saying.
The unidentified official told the newspaper he spoke because of anger over the treatment of the prisoners.
Pentagon officials would not comment on the details of the Guantanamo allegations, the Times said.
The defence department said in a statement quoted by the Times that the military was providing a "safe, humane and professional detention operation at Guantanamo".