The deputy heads are the CEOs of the department, so they're also kind of the accounting officers as well. They rely on or they have a chief financial officer in just about all cases.
I'm not the money expert—I'm not the comptroller general—but for any kind of money there is a due diligence process between central agencies and departments. Anything that's being signed off has to be audited and attested to.
I don't know if you have a specific case in mind.