It is not known whether the U.S. warship cut short its visit or left as planned. According to some sources, it was to have stayed until Saturday.
The USS Mount Whitney arrived on Thursday after a three-hour delay. Sources in the local administration said that the U.S. warship's captain had to complete the paperwork required to cross the state border.
The Blue Ridge class ship is a command and control vessel that is coordinating a group of NATO ships presently in the Black Sea, including two U.S., one Spanish, one German and one Polish ship.
About 80 people gathered at the port to protest the warship's arrival and NATO's presence in Sevastopol. Anti-NATO protests are common in Ukraine's Crimea.
Sevastopol communists previously said they would "block the NATO warship" and that "the Americans will rue the day they set foot in the city."
Ukraine's pro-Western leadership has been pursuing NATO membership since President Viktor Yushchenko came to power in 2004. Ukraine failed to secure a NATO Membership Action Plan, a key step toward joining the alliance, at a NATO summit in April, but was told the decision would be reviewed in December.
Opinion polls regularly show that the majority of Ukrainians are against NATO membership for the country, a former Soviet republic.