The Natural History Museum, the National Portrait Gallery and Tyne and Wear Museums have been chosen to pilot a new system of peer review and self-assessment beginning in the autumn.

The Department for Culture, Media and Sport (DCMS) is trialling the scheme as part of its response to the McMaster report on excellence in the arts, which recommended moving away from government-set targets. It is hoped that once the scheme has been tested in the pilot organisations, it will be rolled out to all national museums from April 2009.

Michael Dixon, the director of the Natural History Museum, said he welcomed the move away from targets and was pleased to be involved in the pilot. "DCMS has selected three representative institutions - a large national, a smaller national and a regional."

He added that he hoped the DCMS would devise a system to look at whether individual institutions were successfully delivering against their corporate plans. "Peer review shouldn't be used to make comparative judgements between institutions. It should track an individual institution's progress," he said.

The DCMS has already scaled back the number of performance indicators in its funding agreements with national museums for the next three years.

In a statement, the DCMS said that the new funding agreements represented a "light touch" approach and that it would no longer be asking for explicit numerical targets in areas such as visitor numbers.

National museums will still have to provide performance data under 12 headings and will also be able to nominate six measures of their own choice.