It is feared that advisers who have previously worked in a school may not make impartial judgments.
OFSTED has said that if it can be proved that an inspector has a connection with a school, then an inspection is "very likely to be invalidated". Its guidance to registered inspectors says inspecting and advising a school simultaneously is unacceptable.
The NAO says OFSTED received seven complaints about inspectors' connections last year, and knew of around 30 others resolved by registered inspectors.
The two agencies say they have agreed on extra guidelines to reduce the risk of unfair and biased inspections.
From next January, all inspection team members will have to declare any interest they have in the school to be inspected. And revised guidance will also make it clear that schools can complain about individuals when they see the team's CVs at the start of the process.
The new requirements were welcomed by Phil Mortimer, a former auditor from Bognor Regis, West Sussex, whose letters to OFSTED, the parliamentary ombudsman and now the NAO have resulted in the changes.
But he remains concerned that many schools will not complain about advisers coming in as inspectors, partly because they believe advisers will report favourably.
An inspection team due to visit a West Sussex secondary school is to include a humanities adviser who has previously been in the school as a subject area adviser.
A spokesman for the school confirmed he knew some of the team members, adding: "West Sussex operates an advisory service and has worked with us over a period of years. We are fortunate to have a good set of advisers and we have made use of them. My personal opinion is they are as objective as any set of inspectors. I believe their integrity is without question."
Mr Mortimer believes such connections are far more frequent than the seven complaints to OFSTED suggest.