The House speaker, Nancy Pelosi, announced on Wednesday that she would veto the two top Republican appointments to the new House select committee investigating the Capitol attack, saying the Trump-allied congressmen could threaten the integrity of the investigation.

But the move sparked the immediate prospect of a boycott from the other Republicans picked by their party to serve on the committee and a threat that they would set up their own inquiry of the events of 6 January.

The top Democrat in the House said in a statement that she was rejecting Republicans Jim Banks and Jim Jordan from the panel because of their remarks disparaging the inquiry and their ties to Donald Trump, who will be the subject of the select committee’s investigation.

Pelosi said her move was an unprecedented but necessary step given the gravity of the select committee’s inquiry into 6 January, when supporters of the former president stormed the Capitol in a violent insurrection that left five people dead and nearly 140 injured.

“I must reject the recommendations of Representatives Banks and Jordan to the select committee,” Pelosi said. “The unprecedented nature of January 6 demands this unprecedented decision.”

The move also demonstrated Pelosi’s far-reaching and unilateral authority to steer the direction of the investigation. Pelosi made her decision after deliberating with her leadership team and her picks for the panel, according to a source familiar with the matter.

The Republican House minority leader, Kevin McCarthy, had included Banks and Jordan – both outspoken Trump allies who voted against certifying Joe Biden’s election victory – among his picks on Monday, foreshadowing a bitter partisan fight over the direction of the inquiry.

The top Republican in the House slammed her move as an “egregious abuse of power” that would “irreparably damage this institution”, and threatened to withdraw Republicans from the investigation unless Pelosi reversed course and installed all five appointments.

“This panel has lost all legitimacy and credibility and shows the speaker is more interested in playing politics than seeking the truth,” McCarthy said. “Republicans will not be party to their sham process and will instead pursue our own investigation of the facts.”

Still, Congresswoman Liz Cheney, the one Republican member picked by Pelosi to serve on the select committee after she castigated Jordan on the House floor on 6 January, blaming him for the attack, told reporters that she supported Pelosi’s decision.

“I agree with what the speaker has done,” she said.

The decision by Pelosi to block the pair from serving on the select committee came after a series of calls between Pelosi, her leadership team and the Democratic caucus on Tuesday morning, the source said.

House Democrats were outraged with Banks’s appointment in part because of a statement released on Monday night in which he inexplicably blamed the Biden administration for its response to the 6 January attack, which took place during the Trump administration, the source said.

Banks also drew the ire of Pelosi and House Democrats after he arranged a trip for House Republicans to join Trump at a recent event at the southern border alongside an individual who participated in the Capitol attack itself.

Pelosi also expressed deep concern about the selection of Jordan, the source said, especially given he may have spoken to Trump as rioters stormed the Capitol and disparaged attempts to investigate the deadliest attack on the Capitol since the war of 1812.

The chairman of the select committee, Bennie Thompson, previously told the Guardian that any conversations that involved Trump on 6 January would be investigated by the panel, raising the prospect that Jordan would end up examining his own conduct.