Ukraine's navy says five people were killed. The BBC has been told no-one from either delegation was hurt.
Mr Mitsotakis said the pair heard the sound of sirens and explosions.
President Zelensky said Russia had "either gone crazy or they don't control what their terrorist army is doing".
During a joint news conference, the Greek prime minister said "we heard the sound of sirens and explosions that took place near us. We did not have time to get to a shelter."
"It is a very intense experience... It's really different to read about the war in newspapers, and to hear it with your own ears, see it with your own eyes," he added.
Mr Zelensky said the strike had left "dead and wounded", but said he did not have figures.