The Norwegian driver is 13.3 seconds behind his fellow SKODA Fabia driver after beating his time by 1.3s on the 18.43-kilometre Pindula test.
Championship leader Mikkelsen chose to use intermediate tyres for the morning loop of stages, a decision which cost him some time.
"The stage was a little more damp in the forest section but the slicks were still the way to go," he said. "I tried to push as much as I could."
Hanninen, who had more grip on the slicks - with cuts, necessary on the drying surface - said: “We had a lot of cuts but I think the others had even more cuts.
"It was difficult and the tyres were overheating but we are here. Now we have to flip the coin in service and make the tyre choice the other way.”
Overnight leader Tomas Kostka dropped to third in the standings ahead of Roman Kresta and Jan Kopecky - second in the standings ahead of Hanninen - who continues to lose time on wet tyres.
On the earlier Slusovice circuit stage Hanninen was 6.6s faster than Mikkelsen, who bemoaned afterwards: "It was completely the wrong tyre choice but I was happy with my driving because I was neat as I could be."
The Saturday programme has a total eight stages.