"Employees of the Security Service of Ukraine (SBU) conducted sanctioned searches in the offices of the subsidiary of the Russian company Yandex in Kiev and Odessa", the SBU said in a statement.
The security agency said the searches were part of a treason probe and accused Yandex of passing on the personal details of Ukrainian citizens, including military personnel, to authorities in Russia.
"The information was handed over to the Russian intelligence services for the purposes of planning, organising and carrying out espionage, sabotage and subversive operations in our country," it said.
Yandex confirmed the searches at its offices but said it had no "information" about the activities of the Ukrainian security agency.
"Yandex is ready to provide all information regarding its operations in Ukraine, according and limited by Ukrainian legal procedures," said company spokeswoman Ksenia Korneyeva.
The latest move comes after Ukraine blocked Russia's most popular social media networks and the Yandex search engine earlier this month in response to the Kremlin's alleged backing of a three-year separatist war in the east.
Moscow and Kiev have been locked in a bitter feud since the Kremlin seized Crimea the Crimea peninsula in 2014.
The Kremlin described Ukrainian President Petro Poroshenko's decision to ban its sites as "another manifestation of unfriendly, short-sighted policy toward Russia".
The ban remains in effect for three years.
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