More than half of secondaries and two in five primaries said they and their teachers need more training and guidance to make self-evaluation effective.
The survey of 516 primary and secondary schools was carried out by The TES, the National Association of Head Teachers and Lloyds TSB.
David Bell, chief inspector, announced proposals earlier this year for shorter, sharper inspections with "more reliance on self-evaluation as a starting point".
David Hart, NAHT general secretary, said that training would be crucial to the success of the new regime. "Self evaluation is the future of accountability and schools need funding for training. It is something we will be talking to the Government about," he said.
One in 25 secondaries and a handful of primaries admitted that they have no system of self-evaluation.
The survey reveals widespread concern about inspectors' attitudes to self-evaluation.
One school complained that self-evaluation "seemed to go out of the window" during an inspection, while others said that inspectors seemed to place little value on schools' views.
Concern about the current inspection system was most common among heads of special schools and very small primaries who complained that it is unsuitable for them.
Despite complaints about the paperwork involved, most heads were complimentary about self-evaluation and welcomed the proposed new inspection framework.
Anthony Bolton, head of Herrington primary, in Sunderland, said: "It is surprising and indeed salutary how often self-evaluation throws up information which was previously hidden."
But others were more sceptical. An East Anglian head said: "Are there any heads or schools that do not look at their practice and regularly evaluate? Maybe I am naive but if there are, I have never seen one.
"But what a lot of jobs have been created (in self-evaluation) that serve to take money away from children's education."
The NAHT conference in Cardiff will consider several motions about the Office for Standards in Education this weekend. Delegates will criticise David Bell's assertion that satisfactory is no longer good enough and raise concern about the number of schools judged to be failing.
* The winner of the pound;1,000 prize for the first school survey out of the hat was All Saints primary, Gorton, Manchester. The prize was donated by Lloyds TSB.