Senators on Tuesday rejected building the 700 miles of double-tier border fencing Congress authorized just seven years ago, with a majority of the Senate saying they didn’t want to delay granting illegal immigrants legal status while the fence was being built.

The 54-39 vote to reject the fence shows the core of the immigration deal is holding. The vote broke mostly along party lines, though five Republicans, including Sen. Marco Rubio and the rest of the bill’s authors, voted against the fence, and two Democrats voted for it.

Republicans had offered the fence as a way to build the confidence of voters skeptical that the government will enforce its laws, but opponents said building more fencing is costly, would take too long, and shouldn’t be dictated by Washington.

“I think we should leave that to the best judgment of the Border Patrol,” said Sen. John McCain, one of the eight senators who wrote the immigration bill.

Sen. John Thune, South Dakota Republican, proposed the border fence amendment, which would have prevented the administration from granting any illegal immigrants legal status under the bill until at least 350 miles of double-tier fencing has been erected, and would withhold full citizenship rights until 700 total miles have been built.

Minutes after the border fence, senators also voted to weaken current law that requires the government to have biometric checks such as fingerprints or eye-scans for every visitor to the U.S. — a recommendation of the 9/11 commission that looked into the terrorist attacks on Washington and New York.

Senators said it is too expensive to check fingerprints at all air, land and sea ports of entry. Instead, the bill calls for photographic checks at air and sea ports, but excludes land ports.

“When is our federal government going to keep its promises when it comes to the issue of border security?” said Mr. Thune, the sponsor of the fence proposal.

Mr. Rubio said he supports building a border fence, and pointed to $1.5 billion included in his bill for more infrastructure, which he said will go to a fence plan. Mr. Rubio said Mr. Thune’s amendment didn’t lay out the details for “a specific border plan.”

“Therefore, I will oppose his amendment and instead continue to work with my Republican colleagues to arrive at a new measure that improves on the significant border security measures already in the bill,” the Florida Republican siad.

The border now has 651 miles of barriers, but only 36 miles are at least double-tier fencing. Another 316 miles are single-tier pedestrian fencing, and the rest — 299 miles — are vehicle barriers that still allow wildlife, and people, to cross.

The border fence vote was one of several key showdowns expected as the Senate works on its immigration bill, which grants most of the estimated 11 million illegal immigrants in the U.S. a path to citizenship.

The 2006 vote to build the fence came back to haunt some of its supporters, including Mr. Obama, who was in the Senate at the time. He was harshly criticized by immigrant-rights advocates back home in Illinois, who said they felt betrayed by the vote.

A year after that 2006 vote, however, Republican Sen. Kay Bailey Hutchison wrote legislation giving the Homeland Security Department the option to build less fencing.

Homeland security officials say they are comfortable with the amount and mix of fencing they have now.

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