According to state-owned wine producer Plantaze, Russian authorities have banned the import of its alcohol from Wednesday owing to sanitary failings -- accusations the company denied.
"It is clear that the decision is in the context of NATO membership," said Montenegro's Prime Minister Dusko Markovic.
He said Russian citizens had "lost an opportunity to consume the best wines" owing to the "irresponsible policy" of their authorities.
Montenegro is expected to become a member of NATO later this year and its parliament will meet on Friday to approve the accession.
Russia has expressed strong opposition to the move, describing Montenegro's membership of the Western military alliance as "deeply erroneous".
The 620,000 citizens of Montenegro, on the Adriatic Sea, are mostly Orthodox Slavs and Moscow has long considered the country to be in its sphere of influence.
Plantaze's manager Milan Milutinovic told reporters that 20 percent of its exports usually went to Russia -- adding up to 10 million bottles in the past five years -- meaning the ban would significantly damage sales.
"We export to 42 countries throughout the world, some of which have the strictest quality control, and we have never had such problems," Milutinovic said.
Montenegro's accession to NATO would reinforce the bloc's presence in the Balkans as Greece, Croatia and Albania are already members.