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The measure, passed on a 258-163 vote, won't allow the administration to transfer the detainees from the prison facility at the U.S. naval base in Guantanmo, Cuba to U.S. territory even for trial or indefinite imprisonment.
The move could further hamper the administration's prospect to meet the deadline set by U.S. President Barack Obama to close the prison before Jan. 22 next year.
U.S. Secretary of Defense Robert Gates has already conceded on Sunday that the administration will likely miss its deadline to close the controversial prison.
The Guantanamo prison was opened in 2002, with some 223 detainees left.
The harsh treatment of the detainees and deprivation of the detainees' rights at the prison have hurt U.S. image abroad and there has been an increasing voice for shutting down the prison facility around the world.
On Jan. 22 after he was sworn in as president, Obama ordered to close the prison within one year.
However, his proposals to bring some of the detainees to U.S. soil for trial or imprisonment have met with growing opposition from U.S. public and lawmakers.
The Senate voted in May to block the funds Obama requested for closing the prison, saying he has to present a more detailed plan for the closure first.