Juncker, head of the EU executive commission, on Thursday said that Italy's March 4th elections could produce "no operational government" in Rome and contribute to turbulence on the financial markets.
"I think I was totally misunderstood," Juncker told reporters at a European Union summit in Brussels. "What I said yesterday was misleading and we tried during the course of the afternoon to make it clear."
"As a commission we think that there will be a government which can work after the elections," he added.
Juncker's comments on Thursday were that next week will be very important for the EU because of the Italian vote and the result of a membership ballot of Germany's Social Democrats on whether to join a coalition led by Chancellor Angela Merkel.
"We have to prepare ourselves for the worst scenario," Juncker told a Brussels think-tank. "The worst scenario could be no operational government in Italy."
"Combining all these uncertainties, the SPD, Italian elections, minority governments here and there... we could have a strong reaction on the financial markets in the second week of March, so we are preparing for this scenario," he added.
His remarks were followed by a negative reaction on the Milan stock market before he issued a statement to reassure the public about the Italian elections.
Polls in Italy indicate a coalition between the centre-right opposition Forza Italia party and the far-right, with anti immigrant groups possibly ending up in government. It could result in a parliament without a stable majority.