It's likely that your Dad's former employer is not the one that's paying him the pension, but the pension scheme. Depending on the nature of the pension scheme, the actual pension may be paid from an insurance company. Your first task is to find out who exactly is paying him the pension. Effectively, they are now "his employer" and will operate PAYE in the normal way.
If your father is below the income tax threshold, he / you should contact his local Inspectior of Taxes and get a certificate of tax credits in favour of the pension payer. If he has been incorrectly paying tax, he can reclaim it.