The action in Strilkove appeared to be the first move outside Crimea, where Russian forces have been in effective control since late last month.
There were no reports of gunfire or injuries. The incident raises tensions already at a high level before Sunday's referendum.
In a statement, the Foreign Ministry denounced the foray outside Crimea, and said Ukraine "reserves the right to use all necessary measures to stop the military invasion by Russia."
The village is on a long spit reaching northward from the main part of the Black Sea peninsula, about 10 kilometres north of the border between Crimea and the Kherson region.
A spokesman for the Ukrainian border guard service, Oleg Slobodyan, told The Associated Press the Russians, about 120 in all, took control of a natural gas distribution station in the village.
The Foreign Ministry said the force consisted of about 80 and did not mention the station, but said the village was seized.
As Crimea prepares for Sunday's referendum, dozens of billboards throughout the regional capital proclaim "Together With Russia."
But a few have been hit by spray-painters who scrawled out "Russia" and replaced it with "Ukraine."
The referendum is denounced by Kiev and the West as illegitimate; the West is threatening costly sanctions against Russia if it moves to incorporate Crimea. But the result is seen as a foregone conclusion.
Crimea is almost certain to vote to split off, further aggravating Ukraine's political crisis and one of the harshest East-West confrontations since the end of the Cold war.
At the United Nations, Russia vetoed a Security Council resolution declaring the referendum illegal, and close ally China abstained in a sign of Moscow's isolation on the issue.
Supporters of the US-sponsored resolution knew that Russia would use its veto. But they put the resolution to a vote this morning to show the strength of opposition in the
15-member Security Council to Moscow's takeover of Crimea.