Mr. Mattis would not say whether there were still differences among senior Trump administration officials about whether to send more troops to advise and support Afghan forces. But he acknowledged that he had not used the authority that Mr. Trump gave him in June to deploy nearly 4,000 additional American troops to Afghanistan, saying that he wanted to wait until the larger strategy, and the rationale, for the mission were settled.

“You fight wars for a reason,” he said. “You come up with a political reason for it.”

One contentious issue in the administration’s review concerns how to deal with Pakistan, where the Taliban and the Haqqani network have maintained a sanctuary. The State Department said this week in a report on terrorism that the Pakistani government had “failed to take significant action” to prevent those groups from threatening American and Afghan forces in neighboring Afghanistan.

The Pentagon is withholding $50 million in military reimbursements to Pakistan that it had yet to deliver for fiscal year 2016, signaling displeasure with Islamabad’s failed efforts against the Haqqani network.

This is not the first time the Defense Department has withheld a Pakistani military reimbursement, and Mr. Mattis said it did not mean the Trump administration had settled on a new, tougher stance toward the Pakistanis. “This is an assessment of the current state of play,” he said.

Separately, Mr. Mattis dispelled rumors that Lt. Gen. H.R. McMaster, Mr. Trump’s national security adviser, would be leaving that post for an Afghanistan-related assignment.

He also defended Mr. Trump’s second July 7 meeting with President Vladimir V. Putin of Russia at the Group of 20 economic conference in Hamburg, Germany. That encounter, which some witnesses have said lasted almost an hour, relied solely on a Kremlin-provided interpreter and was initially not disclosed by the White House, has brought sharp criticism of the president. Mr. Trump has said that the discussion lasted far less than an hour.