The announcement, which raises the spectre of a standoff with Russian warships, came hours after Ukraine said it had liberated a village as part of a grinding push against Moscow's forces along the southern front.
Russia issued its maritime threat after scuppering a key deal last month brokered by the UN and Turkey, which guaranteed safe passage for grain shipments from three Ukrainian ports.
Ukraine's Infrastructure Minister Oleksandr Kubrakov said the Hong Kong-flagged Joseph Schulte left Wednesday morning from the port of Odesa -- one of three that participated in the now-scrapped grain export deal.
"The first vessel is moving along the temporary corridors established for civilian vessels to and from Black Sea ports," he said.
Ukraine's President Volodymyr Zelensky welcomed the development. "Ukraine has just made an important step toward restoring the freedom of navigation in the Black Sea," he said on social media.
The Joseph Schulte was en route to Turkey, a maritime tracking website showed as of 1820 GMT.
- Drones batter Odesa port -
Since Russia's exit from the accord in July, it has stepped up attacks on Ukraine's Black Sea port infrastructure and facilities Kyiv uses to export grain through the Danube river.
The governor of the Odesa region said Wednesday that Russian attack drones had damaged grain facilities at a river port near the Romanian border.
The air force meanwhile said it had downed 13 Russian drones over Odesa and the neighbouring Mykolaiv region.
The incident sparked outrage in EU-member Romania -- now a key hub for Ukrainian grain exports abroad since the collapse of the exports deal.
"I strongly condemn the continued (Russian) attacks on innocent people, civilian infrastructure, including grain silos in the ports of Reni and Izmail," Foreign Minister Luminita Odobescu said.
Zelensky, too, condemned the strikes, adding that "every Russian attack on them is a blow to world food prices, it is a blow to social and political stability in Africa and Asia".
"It is unacceptable," said US State Department spokesman Vedant Patel. "Putin simply does not care about global food security."
The possibility of a Russian attack on cargo ships in the Black Sea increased after Moscow said it fired warning shots from a warship at a cargo vessel heading towards Izmail last week.
- Ukraine pushes on southern front -
The Joseph Schulte left Odesa hours after Kyiv announced the capture of Urozhaine, a small village in the industrial east.
"Our defenders are entrenched at the outskirts. The offensive continues," Deputy Defence Minister Ganna Malyar said on social media.
Malyar's announcement comes a day after Russian defence minister Sergei Shoigu said Ukraine's military resources were "almost exhausted", despite receiving Western arms deliveries.
Moscow did not confirm the takeover, saying only that its forces were continuing to engage Ukraine's forces around the village.
The Donetsk region -- which has faced the brunt of fighting in recent months -- is one of four Ukrainian regions the Kremlin claimed to have annexed last year.
Russian attacks in the last 24 hours killed four people and wounded seven, its governor Pavlo Kyrylenko said Wednesday.
Further west of Urozhaine, Ukrainian forces have also been fighting to push back Russian forces from the north and south of the war-battered town of Bakhmut.
Russian troops captured it in May after a months-long battle but immediately Ukrainian forces began clawing back ground around its flanks.
- 'Saboteurs' -
Russian forces have been pushing back in the northern Kharkiv region, spurring local authorities to urge vulnerable residents to evacuate.
"I'm ill, and I have to get my grandson out," 53-year-old evacuee Vira Vunesku told AFP as she readied to leave the frontline town of Kupiansk.
"My condition is serious. I was in a hospital in Kharkiv, came back home for a bit, and now I have to leave again".
Russia's FSB security service said it had "eliminated" four Ukrainian "saboteurs" who tried to cross into Russia's western Bryansk region from northern Ukraine, Russian news agencies reported.
Russia also said its air defence systems had downed several drones overnight near Moscow, in the latest of a string of aerial attacks that have targeted Russia's urban centres.
At an exhibition in the Moscow region, Russia showcased Western military hardware seized from Ukraine.
Among the "trophies", according to the Russian ministry of defence, was an American M113 armoured carrier, an Australian Bushmaster armoured car and a Swedish CV90-40 combat vehicle.
Also in Moscow, a Russian court sentenced a young man to ten years in jail for trying to set fire to a military registration office, independent rights group OVD-Info said Wednesday.
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