Russia hit the Golden Leo - a Guinea-Bissau-flagged ship manned by a crew from India and Syria - with three cruise missiles, causing a fire on Sunday, Ukraine's navy wrote on the Telegram messaging app.
A Reuters witness in Odesa saw smoke billowing from a vessel off the coast on Sunday, which Reuters was able to confirm was the Golden Leo.
A separate Russian attack on Odesa, Ukraine's largest seaport, killed three people and wounded three others on Monday, Serhiy Lysak, head of the city's military administration, said.
He said infrastructure facilities came under attack but gave no further details.
A search and rescue operation lasted all night, Ukraine's seaports authority said, adding that nine crew members and one of its maritime pilots were killed.
Eight of the vessel's 17 crew members were rescued, it added.
Golden Leo is owned by Mumbai-based Ocean Grace Shipping Ltd, according to LSEG data.
Its manager, Friends Shipping Co SA, did not immediately respond to an emailed request for comment.
There was no immediate public comment from Russia on the incident.
The Black Sea was a flashpoint of the Ukraine war in the months following Russia's 2022 full-scale invasion of its neighbour.
But under a deal meant to ease global price shocks and allow both countries to ship grain, shipping had largely resumed.
Russia and Ukraine, however, are now stepping up attacks in the Black Sea and Sea of Azov and targeting key revenue sources.
Ukrainian forces have hit Russian energy infrastructure, including oil tankers, while Russia is intensifying its attacks on Ukraine's deepwater ports and cargo vessels.
Russia's defence ministry said on Monday that its forces hit fuel reservoirs at the port of Odesa overnight, Interfax reported.
Russian strikes have killed 28 people in the Odesa region so far this month, its governor said on Monday.
Both Russia and Ukraine are major grain exporters, and the renewed violence on this route has raised concerns about supply.
Ukraine, which in recent seasons accounted for about six per cent of global wheat exports and about 11 per cent of global corn exports, has lost about a third of its capacity to export grain via its Black Sea ports due to Russian missile and drone attacks, traders and analysts have said.
The Ukrainian attacks have forced Russia, the world's top grain exporter, to limit shipping in the Sea of Azov - a route that handles about a quarter of its grain exports, sources have told Reuters.
