Speaking to Planning after last week's Royal Town Planning Institute (RTPI) Scotland annual conference in Aberdeen, Derek Mackay said he would raise the issue with council chiefs.
The figures for April to June 2012 also showed that authorities took an average of 63 weeks to determine all types of major developments - 47 weeks longer than the four-month statutory timescale. Trade body Homes for Scotland described them as an "outrage".
The Scottish government is considering raising the cap on application fees from £15,950 to £100,000.
However, councils that fail to improve their performance, based on a new government-led Planning Performance Framework, would have the lower cap reinstated.
Mackay agreed that the figures are disappointing and said he will be raising the issue with local government bodies Heads of Planning Scotland and the Convention of Scottish Local Authorities.
"I have made it abundantly clear that there will be no increase in planning fees until I see an improved performance and that absolutely remains my position," he said.
However, Mackay added that the performance statistics "gave a mixed picture", with improvement in some areas but not universally.
According to Mackay, the forthcoming bill on raising planning fees would be examined by Holyrood this legislative year, with the aim of it coming into force next autumn.
He also dismissed a call made at the conference by former RTPI president and consultant Kevin Murray for a freeze on all large out-of-town retail developments in Scotland.
In September, the government announced a review, chaired by architect Malcolm Fraser, looking at how to protect town centres.
Mackay said: "Generally speaking, a national moratorium on any kind of development feels completely disproportionate."
Councils should judge such applications on their individual merits, he said, on the basis of current planning policy to protect town centres.
But Mackay said he was "enthused" by the review and was "working closely" with Fraser on how planning could support town centres.