A money crunch in the Canadian military that temporarily suspended a navy mission is also affecting the air force and forcing it to look for places to trim the budget, CBC News has learned.

As the end of fiscal year approaches, the air force faces a shortfall of $28.1 million. It will balance the books by lowering its fuel stocks and putting off what it calls minor projects.

"But I want to emphasize that no aircraft operations will be affected. There'll be no reduction in flying hours. And aircraft will certainly not be sitting on the ground as a result of the over-programming," Capt. Jim Hutcheson, an air force spokesman, said Thursday.

On Wednesday, the navy said it didn't have the money to send HMCS Halifax on a scheduled sovereignty mission off the East Coast.

Defence Minister Gordon O'Connor later announced the Canadian Forces would reallocate up to $5 million so HMCS Halifax could set sail. It is set to head to sea on Monday. That money will come from somewhere else in the Armed Forces' existing budget.

Some military analysts say the root cause of this cash crunch is the mission in Afghanistan, where Canada currently has more than 2,000 troops. Inside the military, some commanders also say the army's commitment in Afghanistan is putting pressure on the other branches of the Armed Forces.

"With the commitment to Afghanistan, Iraq, … we're seeing countries, not only just Canada, but Great Britain, the Americans also, having to make very hard decisions within where they're spending their military bucks," said Rob Huebert of the Institute for Military and Strategic Studies.

But O'Connor rejected that argument.

"The Afghan mission is budgeted quite separately. The air force, army, navy and other elements of the Armed Forces have their budgets each year," he said.

"Afghanistan is managed separately."