If CIC asks for N.o.c from your department and they don't give it. You can simply write to CIC explaining the same.
Usually they only require police certificates to make sure you don't have a criminal history. Just because you work for the Government of your home country does not make you ineligible for PR. There is a specific section that asks about Government Positions held for applicants like you. They may do additional checks and verification, but I don't think they have any reason to refuse your application unless there are some serious security related issues.
You may or may not have some trouble getting reference letters for the time you worked at the University(but that's a different matter all together).