The government's response in the draft Public Audit Bill is "designed to ensure" the independence of the Auditor General according to Finance Minister Jane Hutt.
Ms Hutt made the comment during her statement on the introduction of the bill.
The bill intends to reform and modernise the governance of the Wales Audit Office (WAO) and the position of the auditor general for Wales.
It will establish a WAO board made up largely of non-executive members appointed by the PAC.
Wales Auditor General Huw Vaughan Thomas has criticised the draft bill as he believes the independence of the auditor general could be constrained by the requirement.
Mr Thomas has suggested that the auditor general should be able to continue to employ their own staff and procure their own professional services.
However, Ms Hutt said that clause 26 of the government's response to the bill is "designed to ensure that it's the auditor general of Wales who determines his or her own work programme to maintain the independence of the office".