Senate Republicans are facing criticism over their last-minute decision late Friday to keep the corporate alternative minimum tax in their tax bill to help pay for other tax breaks.

The GOP added the corporate AMT back into the bill to raise $40 billion over 10 years to help pay for bigger breaks for noncorporate businesses and a deduction of up to $10,000 for state and local property taxes. Leaders made those changes to gain the votes of a few holdout GOP senators.

On Monday, the U.S. Chamber of Commerce called the retention of the minimum tax a "bombshell" and a "very unpleasant surprise."

Keeping the AMT "eviscerates the impact of certain pro-growth policies like the R&D tax credit and exacerbates the international anti-abuse rules," Chamber vice president for tax policy Caroline Harris wrote in a blog post. "This cannot be the intended impact from a Congress who has worked for years to enact a more globally competitive tax code."

The business group has supported the GOP tax effort and had issued a statement praising the late-night passage of the Senate bill.

The last-minute change to keep the corporate AMT is shaping up to be one of the less viable provisions of the Senate bill as Republicans aim to reconcile it with the House version in conference.

"I think that has to be eliminated because that would destroy R&D," said House Majority Leader Kevin McCarthy in a Monday morning interview on CNBC.

"That should be eliminated for sure," he said, even as he downplayed other differences between the two bills.