WASHINGTON—Senate Republicans, in their push to pass a sweeping tax bill, undermined a research-and-development tax credit many companies use to encourage innovation, and business interests are in revolt.

Late Friday, just hours before the Senate voted for the bill, Republicans decided to preserve the corporate alternative minimum tax instead of repealing it as planned. The change gave them money for lawmakers’ other priorities, but it could force many companies to lose tax breaks the bill’s authors intended to protect.

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