So much for weeding out special breaks in the tax code.

The House Ways and Means Committee — Congress’s chief author of tax laws — advanced legislation Thursday that would extend a tax credit for nuclear power, saying facilities in the works in the southeastern U.S. likely need the government subsidy to get off the ground.

The tax-writing panel cleared the legislation from Rep. Tom Rice by voice vote. Mr. Rice, South Carolina Republican, said the extension will provide certainty for new nuclear reactors in the United States and that 12,000 jobs in South Carolina and Georgia would be put in jeopardy without it.

But at a time when lawmakers say they are looking to flatten the tax code, the vote to continue the carve-outs signals just how difficult the GOP’s climb will be.

Rep. Lloyd Doggett, Texas Democrat, questioned what he described as a special handout for the nuclear power industry.

“With ample natural gas and a growing renewable energy industry, nuclear often does not make economic sense unless it gets some special treatment and subsidies or public handouts,” Mr. Doggett said.

He also said “billions” of dollars in subsidies has already been wasted on the nuclear industry elsewhere, and mocked the dire forecasts from his colleagues if the extension isn’t granted.

The Ways and Means Committee is working on a massive overhaul designed to “flatten” the tax code, eliminating most special breaks in exchange for lower marginal rates on both corporate and individual income.

An army of lobbyists is prepared to defend the current tax breaks, though, and always looking to win new carve-outs.

In the case of the nuclear break, it’s been around for years, but applies only to certain “advanced” reactors approved after 1993 and that come online by the end of 2020.

Mr. Rice’s legislation would allow plants that aren’t in service by the original sunset date of Jan. 1, 2021 to take advantage of available credits.

But amid fits and starts from planned nuclear facilities, application of the credit hasn’t gotten past the planning stages. The Joint Committee on Taxation also estimated the new legislation would cost $16 million over a 10-year period — a paltry sum in the grand scheme of federal budgeting.

In March, Westinghouse Electric Company filed for Chapter 11 bankruptcy, leaving already-delayed plans for several new reactors from Georgia Power and South Carolina Electric & Gas up in the air.

Mr. Rice said plants, which had contracted with Westinghouse, will soon face questions from regulators about how to move forward.

“The full availability of the $2 billion in tax credits will be a key factor in the regulators’ assessment of whether to approve plans to continue with these facilities or shut down construction completely,” said Mr. Rice.

Still, the bill has attracted bipartisan support, which includes backing from Democratic congressmen from Georgia and South Carolina, as well as Rep. Earl Blumenauer, Oregon Democrat and a leading environmentalist voice in the House.

“As we think about how to have … low-carbon energy, we’re going to need to have all our tools available,” Mr. Blumenauer said.

To make a point, Democratic Reps. Mike Thompson of California and Bill Pascrell of New Jersey offered their own amendments Thursday dealing with credits for renewable and offshore wind energy, but ultimately withdrew them.

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