Sitting with him in the audience, the 28-year-old looked to be sharing some intimate moments with her Prince.
She later stood up to applaud as he graduated alongside fellow students at RAF Shawbury.
Her presence at a further public event with William only adds to speculation that a royal engagement could be on the cards for 2010.
Flight Lieutenant William Wales's achievement takes him one step closer to becoming an RAF search and rescue pilot.
He was presented with a flying badge by his father Prince Charles, who was acting in his capacity of Air Chief Marshal at the ceremony.
The course, which William completed in December, saw him tackle night flying, advanced and emergency handling, and formation flying.
The Ministry of Defence said he passed with "flying colours".
Next up for the Prince is his first official overseas trip, where he will represent the Queen in Australia and New Zealand.
After that it's back to flight school in Wales, where he'll learn how to manoeuvre the aircraft with pinpoint accuracy, enabling him to rescue stranded mountaineers or swimmers in the worst of conditions.
William's brother Prince Harry is also training to be a helicopter pilot, though in the Army Air Corps.
The brothers are following in their footsteps of their father and uncle, Prince Andrew, who both flew helicopters in the Royal Navy.
Accompanied by The Duchess of Cornwall, Charles paid special tribute to the family, friends and partners at the ceremony for supporting the graduates.
"I know only too well how complicated it can be having a relative or a close friend in the forces, because they are rarely, if ever, around," he said.
"But today is a day, I think, of great pride for all of the parents, not to mention the girlfriends."