The figures were disclosed by the economy secretary Keith Brown in a written answer to Labour MSP Jackie Baillie.
They showed that, in the financial year 2015-16, the airport generated £1,058,727 from hosting the flights.
Over the last three financial years Prestwick has earned almost £3m from the practice.
It has also emerged that, during the first 11 months of 2016, the airport hosted nearly 1700 military flights.
The Scottish Government refused to disclose which foreign militaries the airport has contracts with as the information is considered “commercially sensitive”.
Ministers said the airport operated “on a wholly commercial basis and at arm’s length from the Scottish Government”.
Planespotters have pictured military flights arriving at the base from countries including the United States, Canada and Kuwait over the last 12 months.
The airport was bought by the Scottish Government for £1 in 2013 amid fears that its then owner, Infratil, would close the company.
This was because efforts to find a buyer for Prestwick had failed even though it had been on the market for 18 months.
A Scottish Government spokesman said: “In compliance with European Union State Aid rules, Glasgow Prestwick Airport is being operated on a commercial basis and at arm’s length from the Scottish Government. The senior management team at the airport has been tasked with all aspects of taking the airport forward, including building on existing revenue streams.
“Handling military and private flights has always been, and continues to be, an important part of Glasgow Prestwick Airport’s offering.”
A Glasgow Prestwick Airport spokeswoman said: “The newly formed executive team are working to deliver an airport that is profitable and sustainable for the long term. The team is looking to grow and develop across all business areas. This includes passenger and cargo aviation, property, training and fixed base operations (FBO).
“Our FBO team facilitate tech stops, training flights, de-icing, fuelling amongst many other aviation related services for executive and military customers.
“Glasgow Prestwick Airport is one of many FB operators across the UK to provide these services to military forces that have obtained clearance from the UK Civil Aviation Authority. However, we believe that our excellent facilities and a skilled workforce will enable us to win more of this business and that we will grow this revenue stream year-on-year.
“Our FBO team manage requests from military customers in the same way they would any private customer.”
Last month, the Scottish Government confirmed the bailout of the South Ayrshire airport would reach £40m in the financial year 2017-18.
Spending watchdog Audit Scotland originally estimated such a level of taxpayer funding would not be reached until 2021-22.