"The data available to me indicate that most of the major municipalities may be added to the red list as early as Monday," he told a news conference.
The updated list is to be released later on Friday.
The government has decided to group municipalities into three categories – green, yellow and red – based on their coronavirus infection risk levels.
Municipalities in the green zone are not subject to any restriction and those in the yellow one have to follow certain recommendations.
Red-labelled municipalities are subject to quarantine restrictions, including mandatory wearing of facemasks, limiting public events and customer flows at shops, and switching to working from home.
On Wednesday, the government decided to place 12 municipalities under local quarantines as of Monday. These are Elektrenai and the districts of Joniskis, Jurbarkas, Kelme, Klaipeda, Kretinga, Marijampole, Pasvalys, Plunge, Skuodas, Siauliai and Svencionys.
Quarantine restrictions will come into effect on Monday and will last until November 9. The district of Raseiniai District was placed under quarantine earlier this month.