The Australian National Audit Office said yesterday the success of the scheme, which has so far delivered $322 million in rewards payments to the states and territories, had been ''mixed''.

When the then Rudd government introduced Literacy and Numeracy National Partnerships in 2008, it was one of the first times the government had tied performance targets to financial incentives.

But, Auditor-General Ian McPhee said in his report yesterday, it was far from clear the money had been well spent, and there was no evidence the money had lifted students' scores in NAPLAN testing.

''ANAO analysis of NAPLAN data from 2008 to 2011 indicates that the LNNP is yet to make a statistically significant improvement, in any state, on the average NAPLAN results of schools that received LNNP funding, when compared to schools that did not receive funding,'' Mr McPhee wrote. He said the states had been paid their bonuses before demonstrating that student performances had improved.

''The first tranche of facilitation payments occurred prior to the signing of the bilateral agreements,'' Mr McPhee found. ''DEEWR [the Department of Education, Employment and Workplace Relations] advised that payments were made at this time so the implementation of the LNNP was not further delayed.'' Nor were ''explicit records'' kept of the process to approve spending proposals.

''Nonetheless,'' Mr McPhee found, ''payments made under the LNNP were soundly based.''

Across Australia, about 10 per cent of government and non-government schools - some 1050 in total - took part in the scheme.

Education Minister Peter Garrett and the Australian Education Union defended the programs yesterday, insisting they had brought positive effects to the schools involved.

Mr Garrett's spokeswoman said it could take several years for the effects to be felt.

''Overall, there have been positive signs that the LNNP is making a difference for students falling behind in participating schools,'' she said. ''For example, between 2008 and 2011, schools participating in the National Partnership had a higher proportion of students above the national minimum standards for NAPLAN in both year 3 reading and year 5 numeracy.''

She said a COAG Reform Council report in April that found the LNNP had lifted overall reading and numeracy results of participating schools.

However, that report showed that in NSW reading and writing scores for year 3 and year 5 students had dropped, and NSW missed out on $35 million in funding for literacy and numeracy programs after failing to meet its targets under the partnership.

Victoria met its targets to lift performances and took its bonus.

Mr McPhee said the education department was ''not in a position to be able to verify the accuracy of the performance results against reform targets'' because of inconsistencies in data collection.

AEU federal president Angelo Gavrielatos said, ''The direct evidence from principals, parents and teachers is that it has been a great success.''