Stephane Bancel told Britain's Financial Times that current vaccines were not likely to be as effective against it.
He also warned it could take months to begin shipping a vaccine that works against the new variant.
Bancel's comments drove fears that vaccine resistance could lead to more sickness and prolong the health crisis.
European stocks fell around 1.5% in early trade after the comments.
The pan-European STOXX 600 dropped to its lowest level in almost seven weeks.
It comes just days after the index saw its worst single-day performance in more than a year on Friday (November 26).
Oil stocks fell over 2.6%, while crude oil futures shed more than two dollars.
European travel stocks, which have been battered during the health crisis, also lost more than 2.5% Tuesday.
Asian shares had seen similar drop-offs.
Japan's Nikkei wiped out early gains and hit its lowest level since October 7.
The country, like Israel, has closed its borders to foreign visitors.
Moderna did not reply to Reuters about when it expects to have data on the vaccine's effectiveness against Omicron.
