Defending Intercontinental Rally Challenge champion Mikkelsen said marker poles by the side of the road in one section had gone since the reconnaissance, making his pacenotes less effective, after dropping to third overall.
"They were not correct at all and I lose so much time in the last part because I had no cuts left in my tyres," said Mikkelsen, 11.1s adrift of first place.
Local hero Jan Kopecky, fastest on the stage, reported a "very big moment" on a slippery section in a third factory SKODA Fabia. The Czech is now second, 2.4s behind team-mate Hanninen.
“It was such slippery tarmac that many times I was just a passenger,” said Hanninen. “It was not fun anymore and I was slowing down because it’s easy to go off. It was like driving on ice with slick tyres."
Mikkelsen topped the timesheets on stage six, the first 11.38km Lukov run.
Kopecky, chasing a third victory on the all-asphalt event, got himself back in contention by claiming the fifth stage.
“It’s raining and we’re on slicks but still it’s quite okay so something strange is happening,” he said after the 18.43km rain-hit Pindula test.
“It was very muddy in a few places.”
Stage four, the second run through Slusovice, was won by Mikkelsen to take a lead he would hold until stage seven.