Democrats on Thursday moved ahead with a confirmation hearing of Alejandro Mayorkas to the No. 2 position in the Department of Homeland Security despite a Republican boycott of the meeting and an ongoing investigation into President Obama’s appointee.

Mayorkas, a top immigration official, unequivocally denied any wrongdoing in the face of reports that he helped a technology company secure U.S. visas for Chinese nationals. Democrats, too, sought to stomp out allegations that Mayorkas ran afoul of the law as they look to fill the department's 15 vacancies in senior positions, including the top two posts.

But Senate Republicans, who protested the hearing by not attending, planted severe doubts that Mayorkas’ confirmation will advance before the inspector general's investigation of him concludes.

“Holding this hearing in light of an active investigation into serious, relevant allegations of professional misconduct by the nominee … appears to be virtually without precedent in the history of this or any other Senate committee,” said Sen. Tom Coburn, R-Neb., the top Republican on the Homeland Security and Governmental Affairs committee.

The year-long investigation alleges that while Mayorkas was director of U.S. Citizenship and Immigration Services, he used his office to help Anthony Rodham, the brother of former Secretary of State Hillary Clinton, and Terry McAuliffe, a Virginia gubernatorial candidate and former Democratic Party fundraiser. Mayorkas is accused of securing EB-5 visas for individuals who wanted to invest in McAuliffe’s electric car company, the Mississippi-based GreenTech Automotive.

The EB-5 visa program allows foreign nationals to invest $500,000 to $1 million in a U.S. company in exchange for a green card. If the companies meet certain job creation criterias, the foreign investor could become eligibile for citizenship.

Mayorkas did not learn of the investigation until this week and has yet to be questioned by the inspector general about it, he said.

Mayorkas testified Thursday that he was asked several years ago to meet with McAuliffe about complaints about the EB-5 program. When asked if he used his influence to help McAuliffe after the meeting, Mayorkas said “absolutely not.”

“I do remember returning to the office and complaining about the fact that I had to hear complaints,” Mayorkas said. “That is all.”

Mayorkas said he continued to hear complaints until this year from McAuliffe and Gulf Coast Funds Management, the company owned by Rodham and used by McAuliffe to help secure the visas.

Mayorkas sticky confirmation process creates a mess for Obama and the Department of Homeland Security. Out-going Secretary Janet Napolitano's departure leaves a void at the top of one of the federal government’s largest agencies, which is deeply involved in a number of issues, including the ongoing immigration debate and persistent terrorism concerns.

It also creates problems for McAuliffe, who at one time boasted GreenTech as evidence of his business acumen, in his high-profile gubernatorial race against Republican Ken Cuccinelli. The Democrat has defended the 20-year-old EB-5 visa program.

A request to McAuliffe’s campaign for comment was not immediately returned but on Tuesday a McAuliffe spokesman said “the investigation [into Mayorkas] does not involve Terry and we hope that it is completed in a timely matter.” McAuliffe’s name came up five times at the tail end of Thursday’s hearing — a meeting that consisted entirely of Democrats.

If confirmed, Mayorkas would lead the DHS until Napolitano’s replacement is found. The highly politicized process of confirming Obama nominees coupled with Mayorkas’ troubles, however, means DHS could be without a leader or second in command for many more months.

That is a chief concerns to Democrats, who were critical of Republicans for holding up Mayorkas’ confirmation based on unproven allegations.

“Rather than allowing rumor and speculation and innuendo to rule the day, this hearing will allow us to continue the process of vetting this nominee,” said Sen. Tom Carper, D-Del. “How can we honestly expect the Department of Homeland Security to effectively and efficiently carry out its mission … without strong and stable leadership?”