The Black Sea is a crucial trading route for Ukraine, one of the world's largest agricultural producers and exporters, but was turned into a naval battleground when Russia invaded its neighbour.
"Russia launched a strike on an ordinary civilian vessel in the Black Sea right after it left Ukrainian territorial waters," Zelensky said in a post on social media on Thursday, adding that there were no casualties.
In a later statement, the Ukrainian navy said the ship was hit with a cruise missile at 11:03 pm (2003 GMT) on Wednesday.
"As a result of the attack, the bulk carrier AYA, which was transporting grain from the Ukrainian port of Chornomorsk to Egypt and was in the Black Sea at the time, was severely damaged," the navy said.
Andrei Ene, a spokesperson of the Romanian coast guard, told AFP that the vessel "did not enter Romanian territorial waters", adding that the ship was "functional, (and) floating".
About 30 nautical miles (55 kilometres) off the Romanian village of Sfantu Gheorghe, the vessel's shipmaster had transmitted a radio message overnight, revealing there had been an explosion on board, the coast guard said in a statement.
So far, the ship has neither requested assistance, nor "entry into the Port of Constanta", Romanian Naval Authority spokeswoman Irina Puscasu told AFP.
Zelensky called for global condemnation of the attack.
"Domestic stability and normal life in dozens of countries around the world are dependent on the normal and unhindered operation of our food export corridor," he said.
Moscow last year pulled out of a UN-brokered deal guaranteeing safe passage for Ukraine's agricultural exports on the Black Sea, but Kyiv has carved out a maritime corridor allowing trade to continue.
More than 5,000 ships have sailed through the grain corridor since it was created, Defence Minister Rustem Umerov said on Wednesday.
Global food prices shot up when Russia invaded Ukraine amid fears conflict in the Black Sea would hobble supplies.
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