The head of the federal agency investigating Karl Rove's White House political operation is facing allegations that he improperly deleted computer files during another probe, using a private computer-help company, Geeks on Call.

Scott Bloch runs the Office of Special Counsel, an agency charged with protecting government whistleblowers and enforcing a ban on federal employees engaging in partisan political activity. Mr. Bloch's agency is looking into whether Mr. Rove and other White House officials used government agencies to help re-elect Republicans in 2006.

Recently, investigators learned that Mr. Bloch erased all the files on his office personal computer late last year. They are now trying to determine whether the deletions were improper or part of a cover-up, lawyers close to the case said.

Mr. Bloch had his computer's hard disk completely cleansed using a "seven-level" wipe: a thorough scrubbing that conforms to Defense Department data-security standards. The process makes it nearly impossible for forensics experts to restore the data later. He also directed Geeks on Call to erase laptop computers that had been used by his two top political deputies, who had recently left the agency.

Mr. Bloch was a loyal member of the Bush administration, serving in the Justice Department's office of faith-based programs, when the president named him to head the Office of Special Counsel in 2003. Unlike many administration appointees, Mr. Bloch doesn't serve at the pleasure of the president. He has a fixed five-year term and may be removed only for malfeasance. That is supposed to ensure his agency has the independence to pursue any probe.