Answering questions about civil liberties and the war on terrorism before the Senate Judiciary Committee, Chertoff confirmed that Justice Department officials had not been consulted as the DOD drafts rules to conduct the tribunals.
The tribunals, if used, will decide whether to put suspected terrorists to death without judicial review.
Some members of the committee expressed dismay that Pentagon officials are drafting rules for picking lawyers, establishing the grounds for justice, and selecting the venue without input from the Justice Department.
"Is the Department of Justice involved in drafting those rules?" Sen. Arlen Specter asked Chertoff.
"The president has committed the responsibility for drafting these rules, in the first instance, to the Department of Defense," Chertoff replied.
"So, the answer is, 'no,'" Specter said.
"At this point, the answer is that the Department of Defense is," Chertoff said.
"It seems to me the Department of Justice ought to be involved. Yours is the department which has the traditional long-standing experience here," Specter said.
Chairman of the Senate Armed Services Committee, Sen. Ted Kennedy, D-Mass., said his committee would ask Defense Secretary Donald Rumsfeld to testify on the tribunals.
Chertoff said he had full confidence that, "the Department of Defense is going to produce a set of rules that comports with those standards that the president has laid down."
The exchange comes as Senate committees, controlled by Democrats, are launching a series of hearings designed to closely look at how civil liberties are protected as the war on terrorism moves forward.