However, Michael Matheson dismissed reports his officials had said the bridge could not cope with the traffic.
He said nearly 80,000 vehicles a day had used the Fife-Edinburgh crossing over the Forth since 2017, but that was "less than capacity".
"It's wrong to say the bridge is at capacity."
The comments follow Scotland on Sunday revealing last month that one million extra journeys had been made over the crossing in the last year, reaching 28 million in the 12 months to last October.
That came despite the Scottish Government pledging that increased cross-Forth travel would be by public transport instead.
Transport Scotland chiefs later admitted the rising traffic level was "not the direction we want travel to go in".
Mr Matheson said: "At peak times, there will be periods of congestion when traffic volumes are at their highest level", which he said would continue.
He said the first evaluation of the new bridge, which opened in August 2017, was due in the spring.
The cabinet secretary said efforts would continue to encourage more people to use buses on the adjacent Forth Road Bridge, which has been designated as a "public transport corridor" and also carries taxis, cyclists and walkers.
Mid-Scotland and Fife Labour MSP Alex Rowley said: "It's not just at peak times the bridge clogs up. We need to fix that."
But Mr Matheson told him the crossing was to provide a more resilient Forth crossing rather than extra capacity.