The department's Bureau of Alcohol, Tobacco, Firearms and Explosives, which lost track of more than 1,000 firearms after they crossed the border, found itself under fire when two of the lost weapons turned up at the scene of the killing of U.S. Border Patrol Agent Brian Terry in December 2010.
Terry's family has been among critics of the Justice Department's handling of the case.
On Tuesday, Sen. Chuck Grassley, R-Iowa raised the matter in his opening statement and again in direct questioning of Holder, noting that questions remain almost a year after three whistle-blowers testified before the House Oversight and Goverment Reform Committee about gunrunning.
"Here we are, one year later, and the Terry family is still waiting for answers. They're still waiting for justice," Grassley said, noting assertions by House Republicans that sealed requests for wiretaps under the Fast and Furious program showed top Justice Department officials knew about the questionable operation long before so far acknowledged.
Holder repeated what he told a House committee last week -- that he read the affidavits and summaries and found no incriminating information.
"You reach conclusions on the basis of hindsight," Holder said. "I try to put myself in the place of people actually looking at the material at the time."
Holder has testified at eight congressional hearings on Operation Fast and Furious, and he has consistently maintained that he knew nothing about the flawed tactics until early last year.
The chairman of the House Oversight and Goverment Reform Committee, Rep. Darrell Issa, R-California, said Monday that the panel wants documents that explain why Holder and the Justice Department decided months later to retract a February 4, 2011, letter to Congress that denied any knowledge by senior officials of improper tactics in the gunrunning sting.
The Justice Department slammed the House committee's Monday announcement, calling it "unfortunate and unwarranted."
"From the beginning, Chairman Issa has distorted the facts, ignored testimony and flung inaccurate accusations at the attorney general and others, and this latest move fits within that tired political playbook that has so many Americans disillusioned with Washington," said spokeswoman Tracy Schmaler.
Both Issa and the Justice Department statement said a resolution still could be reached to avoid the contempt measure.
Last week, Holder assigned Ronald C. Machen Jr., U.S. attorney for the District of Columbia and a Democratic appointee, and Rod J. Rosenstein, U.S. attorney for the District of Maryland and a holdover GOP appointee, to lead the investigations into the alleged leaks.
McCain and other Republicans are insisting on a special counsel, contending that investigators within the system would face a conflict of interest in pursuing top government officials.
A recent report in The New York Times provided classified details of what it described as a U.S cyberattack targeting Iran's nuclear centrifuge program sparked the bipartisan outrage.
Other recent possible leaks of classified information included details on the administration's efforts to expand its drone program and Obama's involvement in "kill lists" against militants in Yemen and Pakistan.
The public airing of details surrounding a recently disrupted bomb plot in Yemen by al Qaeda in the Arabian Peninsula also angered intelligence and national security officials.
Republicans noted that some articles cited sources who took part in White House meetings, which they said showed that leaks were coming from administration officials.
Sen. Jon Kyl, R-Arizona, repeatedly asked Holder how two U.S. attorneys could effectively investigate top national security issues involved in White House meetings cited.
Holder insisted the attorneys he named were dogged prosecutors who would follow any lead, no matter where it took them.
Obama has strongly rejected claims that his White House has deliberately leaked secrets to the media, saying the idea was "offensive" and would put Americans at risk.
Graham, however, said Tuesday that the pattern of the administration was to be uncooperative on issues that might embarrass it -- such as Fast and Furious and now the classified leaks.
Holder responded the administration has prosecuted classified leaks more than any previous administration.