Manchin votes against 'Don't ask' repeal, then apologizes

He also suggested that President Obama should just leave the Senate out of the equation and take it upon himself to stop the policy, noting in his statement that some believe it's within Obama's power to suspend the military discharges "if he deems it a matter of national security."

"If this is correct, and the President was to make such an order, while I may disagree with it, I would respect his authority as President to do so," Manchin said in the statement.

Manchin won a special election last month to fill the seat of the late Sen. Robert Byrd (D-W.Va.) and will have to run for a full term in 2012, when he is likely to be a top Republican target.