The Norwegian had built a strong advantage at the front of the field when he was forced to switch his Toksport-run car off. The engine problem follows Rally de Portugal, where he had the same issue.
Mikkelsen opened the defence of his WRC2 title in the strongest way possible, taking back-to-back category wins at Rallye Monte-Carlo and Rally Sweden.
Engine failures in Portugal and Italy will now impact on his end of season tally; WRC2 competition counts six from seven scores.
Toksport team principal Serkan Duru admitted he was waiting to find out more from Škoda.
“We don’t know exactly what was the problem,” said Duru. “We know the road was rutted and there was sand in the ruts. We are waiting for Škoda to make its examination and then we can understand more about this.
“The engine misfired, went to three cylinders and then stopped – this is the same like Portugal. I don’t know. I can’t say any more than this because we have to wait for the report.”
Mikkelsen is now fourth in the championship, 12 points behind leader Yohan Rossel who also failed to finish the Mediterranean event after rolling his Citroën C3 Rally2.
Neither driver will travel to Africa for Safari Rally Kenya, although they are expected to return to action at Rally Estonia in July.
Finland
Italy
Hungary