Section 309 is not applicable to a private company unless it is a subsidiary of a public company.
Therefore, the ceilings (upto 3% of net profit if there is no managing director or whole time director; upto 1% of net profit if there is managing director or whole time director) are not applicable.
I want to take view that as section 309 is not applicable to Pvt.Ltd.Company it means Pvt. Ltd.Co. can pay Commission to its Director irrespective of limit.