She spoke after 14-year-olds fell short of the target of between 60 and 70 per cent achieving the required standard in their English and science national tests. Pupils achieved the standard in Welsh and maths.
Mrs Butler said: "Although there was an underlying improvement there is no denying that the results at key stage 3 are not as good as we would wish and do not reflect the key stage 2 results.
"We need to look critically at the transition between the key stages and how secondary schools make use of and develop the performances being achieved in priary schools."
She said schools and education authorities must work together to identify and solve the problems, with money available from the Assembly's school improvement fund.
Mrs Butler praised 11-year-olds who achieved similar targets in Welsh and maths and exceeded them in English and science.
Seven-year-olds are not currently required to meet targets but between 82 and 90 per cent achieved the appropriate standards in the subjects they are tested on at 11.
Mrs Butler said: "Our 11-year-olds have once again shown what can be achieved and delivered another excellent set of results.
"Our seven-year-olds are showing that the solid foundations being laid are being rewarded at the end of primary school."