President Obama last week nominated Food and Drug Administration official John Roth to serve as inspector general of the Department of Homeland ­Security, attempting to fill a position that has remained vacant for nearly three years.

Roth, who has led the FDA’s office of criminal investigations since last year, would replace acting inspector general Charles Edwards, who is the subject of a congressional investigation resulting from whistleblower allegations of nepotism and abuse of power.

Edwards has denied the claims against him, calling them “false allegations” and “personal attacks.”

This month, Sens. Claire McCaskill (D-Mo.) and Ronald H. Johnson (R-Wis.) said the acting inspector general should resign and that they were working to find a replacement candidate to recommend to Obama.

Lawmakers from both parties have applauded the president for choosing a nominee to fill the inspector general’s role.

“Mr. Roth appears to be well-qualified to serve as IG, and I look forward to sitting down with him and discussing the challenges he’s likely to face if he’s successfully confirmed,” McCaskill said in a statement Monday.

Johnson said he plans to seek assurances that Roth will “restore and maintain the integrity and independence” of the inspector general’s office. “I have heard from dozens of DHS OIG employees, and it is apparent the office is not functioning as it should,” he said.

Homeland Security, which includes the Border Patrol, Coast Guard, Federal Emergency Management Agency, Transportation Security Administration and other agencies, is home to the third-largest workforce in the executive branch.

Lawmakers and government-watchdog groups such as the Project on Government Oversight have criticized the administration for leaving some of the department’s top positions open for extended periods. A Senate filibuster vote last week paved the way for Obama to fill some of those posts, as well as other key roles within the administration.

The party-line vote last week ended a filibuster rule that both parties used at an increasing rate since the start of the George W. Bush administration to prevent confirmation of presidential nominees, often in attempts to win concessions on unrelated matters.

A Senate committee last week approved the nomination of Jeh Johnson, whom the president tapped to head the Department of Homeland Security. The full Senate has yet to vote on whether to confirm him.

Roth led at least two high-profile investigations during his tenure with the FDA. One case resulted in the United Parcel Service forfeiting $40 million in payments from illegal online pharmacies, while the other involved seizing more than 1,600 Web sites that had been selling counterfeit or misbranded drugs.

The Senate Homeland Security Committee has not yet set a date to vote on the inspector general nominee.