Championship leader Mikkelsen, who slid to fifth after the error, had his mishap on the second run through Mesen-Sauvegarde on Friday's fifth stage.
He made up for it by finishing second in SS6, moving fourth overall, but Hanninen won his fifth of six stages on the opening day to consolidate a 26.8 second overall lead from Freddy Loix.
Peter Tsjoen lies third.
"I braked too late going into a junction and was stuck in a ditch for more than one minute," said defending IRC champion Mikkelsen, who is 1:14 off the lead.
"I think one minute is too much to come back but we will see."
Hanninen was less happy with his SS6 performance, as he lost some of his lead on Loix, although he was content with the overall day's work.
"There were a few places where it was tricky with the sun coming down so I had to slow down," said the Finn. "But it has been a good day and I am happy."