The Republican protest is a sign that the anger stemming from the impeachment fight has yet to subside, even after the Senate trial brought impeachment to a close last week.
No Republicans or their staff were present when the hearing gaveled in at 10 a.m. ET, leaving half the room empty.
"Until the Committee prioritizes oversight activities related to urgent and critical concerns, Republican members cannot support distractions from our core responsibilities," the Republicans wrote. "Given this Committee's access to highly sensitive information, it is concerning that you prioritize publicity events rather than the more productive work that occurs in the Committee's classified spaces."
The hearing was unrelated to Ukraine or Russia, with experts who have worked with intelligence and technology testifying about how the government can work with companies to develop new intelligence technologies.
The GOP letter did not explicitly reference the impeachment investigation, and said other House committees could conduct public hearings on "emerging science and technology matters."
But Democratic Rep. Jim Himes of Connecticut, the subcommittee chairman, said at the beginning of the hearing that the subcommittee's ranking Republican, Rep. Chris Stewart of Utah, said that Nunes "felt strongly that his Republican members not engage in the public work of this committee because of some perceived grievance with the impeachment investigation."
Himes apologized for the witnesses for the one-sided hearing, called the GOP decision "as wrongheaded as it is mendacious."
"Even as this committee was the epicenter of the polarizing impeachment debate, this committee has always succeeding compartmentalizing the emotions and arguments of impeachment from the critical work we do," Himes said. "Not so today, that Rubicon has been crossed."
On the other side, Schiff protested Republicans publicly questioning contacts that his aides had in the intelligence community related to Ukraine and President Donald Trump's call with Ukrainian President Volodymyr Zelesnky.
This story has been updated with additional developments Wednesday.