Pakistani officials say they are "deeply dismayed" over reports that the Koran was desecrated at the US detention facility in Guantanamo Bay.
Hundreds of inmates are still being held at Guantanamo Bay
The latest edition of the American Newsweek magazine said such tactics were used to rattle suspects.
It says that US personnel on one occasion flushed a copy of Islam's most holy book "down the toilet".
Pakistan, a conservative Muslim nation, is also a key US ally in its war against terrorism.
Pakistani foreign office spokesman, Jalil Abbas Jilani, told the AFP news agency Pakistan was also concerned about "the highly objectionable and regrettable treatment meted out to the detainees at the Guantanamo Bay detention centre".
Freed Guantanamo prisoners have complained of ill-treatment
Mr Jilani said the reported act of sacrilege had shocked people of every faith around the world.
"The government of Pakistan condemns the incident and demands that an inquiry should be conducted to bring to justice the perpetrators of this shameful act," he said.
Insulting the Koran and Islam's Prophet Mohammed is regarded as blasphemy and punishable by death in Pakistan.
In an interview last week with the BBC's Haroon Rashid, Abdul Rahim Muslim Dost, an Afghan prisoner recently released from the Cuban detention centre, said a number of Arab prisoners had still not spoken to their investigators after three years to protest at the desecration of the Koran by guards.
Mr Dost also said inmates' beards were shaved and the prisoners were shouted at during interrogations.
The US is holding about 520 inmates at Guantanamo Bay, many of them al-Qaeda and Taleban suspects captured in Pakistan and Afghanistan following the 11 September 2001 attacks in the US.