The Scottish government made the statement in an answer to a question from Scottish Greens MSP John Finnie.
Mr Finnie has concerns about the use of Wick John O'Groats Airport for flying the material held at nearby Dounreay to the US.
A number of flights took place in 2016 and more are expected in the future.
The transfers form part of a deal agreed by the UK and US governments.
The airport at Wick, 30 miles from the Dounreay nuclear site, is run by Highlands and Islands Airports Ltd (Hial), a public corporation owned by Scottish ministers.
Material held at Dounreay is being flown to the US in exchange for a type of uranium used to diagnose cancer.
Mr Finnie has raised concerns in a series of questions to the Scottish government about the suitability of the airport and the highly-enriched uranium involved.
In answer to one of his questions, Environment Secretary Roseanna Cunningham said the uranium being flown out of Scotland must be put to "peaceful uses".
She said: "The UK government owns the nuclear materials currently stored at Dounreay and is responsible for any movements of that material.
"Any transfers to the United States are covered by an agreement for cooperation in the peaceful uses of nuclear energy between the European Atomic Energy Community and the United States of America.
"This agreement rules out the military use of any material transferred under its terms."
Ms Cunningham added: "The Highlands and Islands Airports Limited board are responsible for operational decisions, and for the safe operation of Wick Airport."
A UK-US agreement on the transfer of highly-enriched uranium that involves sites in Scotland rules out the military's use of the nuclear material.