The Sunday night protest was sparked by the arrival at the port of Feodosiya of the USS Advantage, which was to take part in NATO Sea Breeze-2006 exercises, Ukrainian naval spokesman Volodymyr Bova said, speaking by telephone from the Black Sea port of Sevastopol.
Russia's NTV television showed several dozen local residents trying to prevent cargo trucks from unloading equipment from a ship, while others held banners reading "Russia is a Friend! NATO is the Enemy!" and accused NATO of trying to open a base on the Black Sea peninsula.
One elderly lady was shown trying to push away a large yellow military truck as protesters applauded.
Bova said the protesters were mostly supporters of a small radical pro-Russian party that fared poorly in March parliamentary elections, along with activists from the Party of the Regions, the election's top vote-getter and an opponent to Ukraine's integration with the alliance.
"We are not building NATO bases in Ukraine," Bova told The Associated Press.
NATO officials refused to comment on either the protest or the operation.
President Viktor Yushchenko has pushed for membership in the alliance, but has met with resistance from many Ukrainians, especially in Russian-speaking provinces. Earlier this year, lawmakers voted to bar foreign troops from participating in military training exercises in Ukraine.
Another Ukrainian naval spokesman, Mykola Nedohipchenko, said the ship had traveled to Feodosiya as part of NATO's Partnership for Peace program.
Communist faction leader Petro Symonenko demanded parliament fire the defense and foreign ministers and said his faction plans to ask prosecutors to launch a criminal case.