"A Ukrainian army repair and upgrade plant has also been put out of order," the ministry said.
Russia on Sunday said its missiles had destroyed a Ukrainian warship and weapons from the United States after a strike on Ukraine's Black Sea port of Odessa, crucial for grain exports.
The strike Saturday came a day after Kyiv and Moscow signed a landmark agreement hammered out over months of negotiations aimed at relieving a global food crisis.
"High-precision, long-range missiles launched from the sea destroyed a docked Ukrainian warship and a stockpile of anti-ship missiles delivered by the United States to the Kyiv regime," the Russian defence ministry said.
"A Ukrainian army repair and upgrade plant has also been put out of order," the ministry said in a statement on Telegram.
Earlier on Sunday, Russia's foreign ministry spokeswoman Maria Zakharova said Russian Kalibr missiles destroyed a Ukrainian "patrol boat" in the strike.
Neither the Russian army nor Zakharova provided evidence to prove the claims. AFP was unable to confirm the claims independently.
On Saturday, Ukraine accused Russian President Vladimir Putin of having "spit in the face" of the deal to unblock grain exports brokered by the United Nations and Turkey.
Zelensky claimed the strikes on Odessa -- one of three designated export hubs under the deal -- showed Moscow could not keep its promises.
But Turkey said Saturday that Russia denied any attack on the port.
"The Russians told us that they had absolutely nothing to do with this attack and they were looking into the issue very closely," Turkish Defence Minister Hulusi Akar said.
Ukraine's Western allies including Britain and the United States condemned the attack.
US Secretary of State Antony Blinken said the attack cast "serious doubt on the credibility of Russia's commitment" to the deal.
The Ukrainian military had said its air defences had shot down two cruise missiles but two more hit the port Saturday.
Zelensky has said that around 20 million tonnes of produce from last year's harvest and the current crop would be exported under the agreement.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)