Bryan Pagliano, the former State Department computer specialist tasked with setting up Clinton's server, did not attend the Republican-led hearing.
His attorneys said in a letter to the chairman of the Oversight and Government Reform Committee that Pagliano will continue to assert his constitutional right not to testify.
Pagliano spoke previously to the FBI under immunity, telling the bureau there were no successful security breaches of the server.
Pagliano also refused to answer questions last year before a House panel investigating the deadly 2012 attacks in Benghazi, Libya.
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"He has never made any statement or taken any action that would constitute a waiver of his constitutional rights and there is no reason for anyone to believe he might suddenly depart from that position," Pagliano's lawyers wrote in the September 13 letter to Rep. Jason Chaffetz, R-Utah, the Oversight committee chairman.
Chaffetz said there will be consequences for Pagliano's refusal to appear and for "thumbing his nose at Congress."
The email issue has shadowed Clinton's candidacy for president, and Republicans have been steadfast in focusing on her use of a private server for government business, with several high-profile hearings leading up to the election.
Congressional Republicans have cast Clinton as reckless with US national security by insisting on using private communications systems at potentially greater risk of being penetrated by Chinese and Russian hackers.
But Democrats insist the sole purpose of the hearings is to undermine Clinton's presidential bid.
"I believe this committee is abusing taxpayer dollars and the authority of Congress in an astonishing onslaught of political attacks to damage Secretary Clinton's campaign for president," said Rep. Elijah Cummings of Maryland, the committee's top Democrat.
Two officials from Denver-based Platte River Networks appeared before the committee but invoked their constitutional right not to testify.