As Republican leaders wrestle Democratic and conservative factions to pass a trade bill Friday, a handful of Republicans are turning on one of their most trusted policy leaders in Washington: Heritage Action.

The campaign arm of the conservative Heritage Foundation alerted members Wednesday night it that as it stands now, it would score against the Trade Promotion Authority, a bill that gives Congress an up-or-down vote on future trade deals the president negotiates. The legislation is a major priority for President Obama as well as Republican leaders.

"This has been building for awhile. Instead of Boehner and others working with us to get the most conservative 218 votes for the trade bill, they went to work with Nancy Pelosi," Dan Holler, a spokesman for Heritage Action told National Journal.

Heritage Action emphasized that it is not scoring TPA negatively because they are opposed to free trade, but because it wants a promise on another agenda item that will embroil the House this month. In May, the group asked House Speaker John Boehner to state publicly that he would let the Export-Import Bank expire at the end of the month. If Boehner does not do that, they will score against the bill. Heritage Action also has qualms about how the Trade Adjustment Assurance bill, which would give benefits to workers displaced from the trade bill, was tied to TPA.

(RELATED: Meet the Newer, Softer Heritage Action for America)

The incident is making a lot of conservative members' heads spin and marks a shift in the organization's tactics, which appear to be more about procedure than substance, they say.

"The whole thing of trying to tie TPA into Ex-Im, I thought was a little far-fetched," said Rep. Blake Farenthold, a conservative from Texas. "That is actually a reversal of what the Heritage Foundation was speaking a few years back on trade."

Many Republicans, from moderates to conservatives, are scratching their heads as to why Heritage Action would score a free-trade bill negatively.

"It's seems a little illogical to me," said Rep. Steve King, a conservative from Iowa who has been a supporter of Heritage and plans to vote "yes" on TPA. "Don't we know that [Ex-Im bank] is not part of this discussion? It is not part of the TPA. Did I miss something?"

Still, few would discount the impact Heritage Action's "no" vote alert could have on the future of TPA.

(RELATED: John Boehner on House Democrats and Trade: 'We'll Do Our Part, and I Hope They'll Do Their Part')

Rep. John Fleming, a member of the conservative Freedom Caucus and one that is still undecided, said Heritage Action's move "alone probably lost some votes for TPA." In what will likely be a tight final tally, those lost votes could make a big difference.

From the beginning, winning over some of the Republican Party's conservatives was a steep climb. Deep distrust in the Obama administration made it hard for Ways and Means Chairman Paul Ryan to make the case to Republicans that a vote for TPA was not a vote of good faith in the president, but instead a vote for congressional empowerment.

"I still don't have confidence in the president, but when we when we talk about Trade Promotion Authority, that authority is Congress's authority. I see it as such," said Republican Rep. Scott Rigell of Virginia.

Ryan and Republican leadership had been working in close communication with outside groups like Heritage to try and ensure they—at the very least—stayed neutral on the bill. When Heritage Action made its announcement, one Republican leadership aide said there was palpable frustration.

(RELATED: Trade Bill in Jeopardy as Democrats Hold Back)

"It is total fiction. No one in this chamber is talking about Ex-Im and trade in the same breath," the aide said. "They have concocted a false pretense to oppose a bill."

Heritage Action says it tried to work closely with Republican leaders, but concluded in the end that they were not willing to make the concessions the group was asking for.

"We have been very clear since May 22 that conservatives should be using this opportunity to leverage TPA and get Boehner and McConnell on the record on Ex-Im," Holler said.

Tom Rooney, a Republican deputy whip, said that while he once relied on the Heritage Foundation's policy papers and leaders when he was a freshman studying up on issues, he's grown tired of many of the outside groups' tactics.

"It just goes to show how, I think, pathetic those groups have become," Rooney said. "We are talking about free trade here. We are talking about stuff that are tenants of our party."

Rooney says that it's "absolute hypocrisy" that Heritage did not score the Senate's trade vote and has now decided to hold the House accountable.

"It is the most absurd thing that I have ever heard that Heritage is scoring a 'no' vote after the Senate has already gotten to vote so they could preserve [Sen. Ted] Cruz's 100 percent record," Rooney said. "They are actually hurting their own cause because you cannot pass the smell test on that."

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