"We have a lot of big issues and challenges ahead as we prepare for a responsible transition," he told reporters on his plane. "That transition has to be done right, it has to be done in partnership with the Afghans (and) with our allies."
Hagel was sworn in last week as heavy cuts loom for the US military, but he said that Americans realised that Afghanistan remained a major conflict zone with US troops fighting against Islamist militants since the 9/11 attacks.
"We have 66,000 troops still at war in a combat zone, that reality is there," he said. "I don't minimise or marginalise anything just because we may be transitioning to a new phase, we're still at war in Afghanistan."
Since taking the helm at the Pentagon, Hagel has expressed concern over the Defence Department's budget being slashed by roughly $46 billion under the automatic cuts triggered by political deadlock in Washington.
"I'm going to Afghanistan first to thank our troops and acknowledge their work," he said on the plane. "It's always important when a new leadership comes in... that we recognise the people who are the ones on the frontlines."
A total of 100,000 international troops are currently deployed in Afghanistan, with all combat forces due to exit by the end of 2014.