The FCA and PRA came into effect last April and it is estimated their total cost will have been 24% higher than the cost of their predecessor in 2012-13.
The regulators attribute this increase to extra front-line staff, additional costs to replace information technology and new IT, support and premises costs.
The audit office has raised concerns about lack of experience among staff.

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More than a third of staff at the FCA have less than two years' service at the regulator and its predecessor, the FSA.
Current levels of staff turnover have resulted in the departures of skilled and experienced workers, with 26% of those who have resigned from the PRA being classed as 'high-performers'.
The NAO report said: "There is a risk that this may begin to undermine industry confidence in the regulators and poses a risk that knowledge within the organisation will be lost."
The NAO said the high costs of running the regulators are set in the context of the potential benefits of them more effectively reducing harm to consumers and limiting future taxpayer liabilities from financial crises.
The NAO added there is currently a good working-level relationship and communication between staff at both regulators – though this will need to be built on to manage potential conflict between prudential and conduct objectives.

Amyas Morse, head of the National Audit Office, said: "These are still early days for the new regulators, and there are encouraging signs that their new approaches are gaining traction.
"Attracting and retaining the right staff are vital to keeping this progress on track, and so both regulators need to tackle this issue.
"In future, we will expect the FCA and PRA to demonstrate that their increased costs are achieving value for consumers and the taxpayer."