"The FSB's statement does not correspond to reality," the Ukrainian Defence Ministry said on Wednesday.
The ministry has described the FSB's statement as an "attempt by Russia to justify the redeployment of its military units" in Crimea.
Earlier on Wednesday, the FSB said in a statement that over the weekend, it prevented several groups of armed "saboteurs", who were members of the Ukrainian Defence Ministry's intelligence forces, from invading Crimea.
An FSB officer and a Russian serviceman were killed in clashes with the "saboteurs", the statement said.
The armed groups were preparing terror attacks on the peninsula's infrastructure, which were aimed at destabilising the social and political situation in Crimea on the eve of federal and regional elections, read the statement.
Last week, the Ukrainian State Border Service said that Russia was building up troops levels along the contact line separating Crimea and Ukraine's southern Kherson region.
Russia has not made official comments on the claim.
The autonomous republic of Crimea and the city of Sevastopol were absorbed into Russia in March 2014 following a referendum, which was recognised by Moscow but rejected by Kiev.
About 9,000 people were reported to have been killed in the conflict in eastern Ukraine that followed the Russian annexation of Crimea.
The US and European Union imposed sanctions on Moscow in response to its seizure of the territory.
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