Miller, head of the National Counterterrorism Centre, was appointed in an acting capacity in place of Mark Esper by President Donald Trump in a tweet on Wednesday.
"As we prepare for the future, we remain committed to finishing the war that Al Qaida* brought to our shores in 2001. This war isn't over. We are on the verge of defeating Al Qaida and its associates, but we must avoid our past strategic error of failing to see the fight through to the finish," Miller said in the letter directed to all Defence Department employees.
Miller went on to say that it was time for the return of troops but did not provide any details.
"We met the challenge; we gave it our all. Now, it's time to come home," the letter read.
Over the course of his presidency, Trump has pushed for the drastic drawdown of troops involved in foreign conflicts as part of a 2016 campaign promise only to be faced with staunch resistance from Pentagon leadership.
Miller, possibly Trump’s last appointment in office, is known as an advocate of ending US foreign involvements.
*Al-Qaeda - a terrorist organisation, outlawed in Russia.