"We certainly condemn such acts and consider them especially unacceptable in relation to the leaders of other states, especially the president of a friendly country like Poland," ministry spokesman Yevhen Perebyinis said at a press briefing on Tuesday.
The ministry hopes that the incident will be investigated properly, he said.
A young man smashed an egg on Komorowski's shoulder during a religious service at the Peter and Paul Cathedral in Lutsk, where the Polish president attended ceremonies marking the 70th anniversary of the Volyn massacre last Sunday.
The man was detained immediately after the incident and was identified as a 21-year-old resident of Ukraine's Zaporizhia region, says Interfax-Ukraine.
A criminal investigation was opened into the incident on counts of hooliganism. The suspect could face a large fine or up to three years in prison if found guilty.
Tests did not detect any alcohol in his blood.
According to the Polish media, the young man was carrying a backpack with a slogan saying Svoboda (freedom).
However, the local branch of the Svoboda opposition party has denied its involvement in the incident.
The Polish president, for his part, has refused to comment on the events.