"This is very alarming news. In fact, our security services prevented an incursion into the territory by a sabotage-reconnaissance group from Ukraine's defence ministry," Putin told Russian news agencies.
Putin accused the authorities in Kiev of "practising terror" and pledged not to leave the deaths of two Russian officers in alleged clashes unanswered.
"From the Russian side there were losses -- two soldiers killed. We obviously will not let such things slide by," Putin said.
"The attempt to provoke an uptick in violence, to provoke conflict is nothing but an attempt to distract public attention."
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Russia's security service said it had thwarted "terrorist attacks" at the weekend in Crimea by Ukrainian military intelligence and beaten back an armed assault.
The FSB said in a statement that one of its officers was killed in armed clashes while arresting "terrorists" on the night of August 6-7 while a Russian soldier died in a firefight with "sabotage-terrorist" groups sent by the Ukrainian defence ministry on August 8.
Ukraine's national security council chief Oleksandr Turchynov blasted the claims as "hysterical and false" and said Moscow was trying to stoke fear in Crimea.
Ukraine's defence ministry dismissed the allegations as "nothing more than an attempt to justify the redeployment and aggressive actions" of Russian forces in the region.