The latest accounts for the airport show passenger numbers have dropped to 624,000, generating a pre-tax loss of more than £9.2 million.
About £40m of public money will have been invested in the airport by year end, which means it will have exhausted its share of state funding five years early, watchdogs say.
Prestwick Airport leaders have now outlined a range of options aimed at reversing the loss. These include attracting more military business.
Airport accounts also reveal that Prestwick had increased military aircraft handling by one-third in the three years to 2016.
Human rights groups have previously voiced suspicions that the airport had been a stop-off point for rendition flights en route to the US.
Police Scotland is still investigating the potential use of Scots airports by the CIA.
Ron Smith, Prestwick’s chief executive, said: “The volume of military movements flying across the Atlantic each and every day is vast, and the ongoing trend for closures of military airfields across Europe is pushing more and more of this business into those commercial airports approved to handle military aircraft.
“Therefore the opportunities for growth in the handling of military flights at GPA (Glasgow Prestwick Airport) are significant. The business development team is heavily focused on building on and establishing new key relationships with the MoD, USAF, RCAF and other air forces worldwide to ensure the airport is firmly at the top of their preferred operational airport lists.”
The accounts show turnover at Prestwick had fallen to £11.5m - down from £12.4m the previous year - as a result of reduced passenger numbers. After tax its operating losses had widened to £8.7m.
The Scottish Government bought the airport in 2013 after former owner, Infratil, failed to attract a buyer having placed the airport on the market for 18 months. Since then, ministers have significantly revised downwards their estimations for passenger growth.
A Glasgow Prestwick spokeswoman said: “Glasgow Prestwick Airport has appointed an operating board and has a new executive team in place who are working to rebuild the business to deliver an airport that is profitable and suitable for the long term.
“We had forecast increased losses in the financial year ending March 31, 2016. This was primarily due to the movement of a number of Ryanair flights to other airports. However, the losses reported are less than what was forecast.”