College of the North Atlantic in Canada is a publicly-funded institution there. Of course the government is going to investigate some sort of financial discrepancy. As for the government over-stepping management, the head of of the college, Jean Madill, resigned because of such. She said that she was never given any control over what goes on in the college, and when something like this happens, all the responsibility falls on her.
As for the allegations of corruption, there is no missing money. All the money is accounted for. An error caused many employees of the college to be paid more than the Qatari government allotted to them. The Canadian and Newfoundland governments are the ones who have to pay it back.

Sources:
The peninsula article
cbc.ca
vocm.com