Lawyers representing some of the detainees being held in Guantanamo had hoped Obama might veto the entire spending bill in order to block the provisions. They are concerned that the language will also make it much more difficult to release detainees that have been cleared for release to foreign countries.
"It would be preferable if this whole bill were vetoed," says Shane Kadidal of the Center for Constitutional Rights.
But Kadidal says it comes down to practicality. "In this situation you have this huge spending bill with this tiny thing attached to it that is problematic.
"Bottom line: I think its pointless for Congress to be intruding in this way and I do think it's unconstitutional for Congress to tell the president that he can't release a detainee, especially someone ordered released by the courts."
Lawyer David Remes, who represents 15 Yemeni detainees, is critical of the president for not doing more to block the legislation.
"President Obama should have taken a much stronger stand on these provisions, not necessarily threatening to veto the entire package but providing the Democrats in Congress with more leadership on the issue."
The spending bill is expected to reach the president by Monday.