"I fully expect to have 535 pieces of legislation before this is over saying: 'Not in my district. Not in my state.' And we'll just have to deal with that when the time comes," Gates told a senate committee on Thursday.
Mitch McConnell, the Republican leader in the US senate, was critical of plans to move detainees to the US mainland, saying they would pose a security risk.
"Communities are going to be upset about this. This is a very important issue and it deals with public safety, as we all know. We haven't been attacked again since 9/11. We like that and we'd like for that record to continue," the Kentucky senator said.
Gates said the Pentagon had asked for $50 million "as a hedge" in case building a facility to hold the detainees was necessary.
|Rights groups have condemned the treatment of prisoners at Guantanamo [GALLO/GETTY]
Officials were also considering allowing some of the 17 Chinese ethnic Uighurs held at Guantanamo to settle in the US, to help encourage other nations to accept some of the detainees, Gates said.
"What I have heard people talking about is our taking some of the Uighurs, probably not all," he said.
"Because it's difficult for the state department to make the argument to other countries they should take these people that we have deemed in this case not to be dangerous, if we won't take any of them ourselves," he said.
Most of the 17 Uighurs held at the prison camp were cleared more than four years ago of being what the US calls enemy combatants.
The US fears they may face presecution if they are sent back to China and has asked other states to give them residency.
US officials are reviewing the files of 241 detainees held at Guantanamo to determine who could be transferred to other countries or tried in US civilian courts or special military tribunals set up under George Bush, the previous US president, Gates said.
About 60 detainees have been cleared of wrongdoing and the previous administration had planned to charge about 80 of the detainees.