Russia's public health chief Gennady Onishchenko said the ban on one of Moldova's main export earners, due to come into force on Wednesday, had been imposed because Moldova had consistently failed to act to improve the quality of its produce.
"We don't intend to act as a nanny for the Moldovan economy," Onishchenko said in Moscow, according to Interfax news agency.
"The ban is a necessary step that we have undertaken reluctantly, but it is the only possible way of solving the present situation," he said. "There have been violations in technical preparation, storage and end-production."
In Chisinau, Economy Minister Valerii Lazar said the Moldovan side were unclear about the reasons for the Russian move.
"We will have to clarify where technical problems about the quality of Moldovan wine end and where political aspects begin," he told Reuters.
Moscow is unhappy with Moldova's drive to conclude political association and free trade deals with the European Union in November in preference to expanding ties with Russia.
A Kremlin envoy this month warned that Chisinau's policies could bring retaliation from Moscow, possibly involving cuts in Russian gas deliveries, on which Moldova relies heavily.
Moldova's neighbor Ukraine, another former Soviet republic, has also come under pressure from the Kremlin to halt its European integration plans.
Exports of wines and spirits such as cognac and vodka are a big currency earner for Moldova - which has a population of 3.5 million and is one of Europe's poorest states.
Sales to Russia, the main market for its alcoholic drinks, brought in some €100 million last year.
Despite pressure from Russia, both Moldova and Ukraine are looking to a November summit in Vilnius, Lithuania, to lock in place landmark agreements with the EU.