Ukraine's state security service searched the Kiev offices of Russia's state-run RIA Novosti news agency and TV channel RT on Tuesday, after detaining one journalist near his home, officials said.
"Investigative actions are continuing, there are searches in RIA Novosti and other media structures," Olena Gitlyanska, a spokeswoman for the SBU security services told AFP.
On her Facebook page, Gitlyanska said Russian-controlled media were being "used as tools in a hybrid war against Ukraine."
Earlier the day, RIA Novosti reporter Kyrylo Vyshynsky was detained by Ukrainian law enforcement officers near his house.
The raids and detention came just hours before Russian President Vladimir Putin was to open a bridge that will provide the first direct road connection to the Crimean Peninsula which Moscow annexed from Ukraine in 2014.
"Kiev decided to take revenge on us for the Crimean bridge," Margarita Simonyan, RT's editor-in-chief, said on her Twitter feed.
The Kremlin called the raid "scandalous".
"If it is the case that the actions of Ukrainian law enforcement bodies are somehow connected with the professional work of these media organisations, that would be outrageous and scandalous," Kremlin spokesman Dmitry Peskov told journalists.
According to the SBU, RIA Novosti and RT share the same offices in the centre of Kiev.
Up to 15 journalists work for RIA Novosti in Ukraine, some of whom transmit information to its headquarters in Moscow while others, led by Vyshynsky, are in charge of the ria.com.ua website for the Ukrainian audience.
Russia and Ukraine have been locked in a bitter feud since the 2014 Crimea takeover.
Moscow has been accused of fuelling a rebel conflict in eastern Ukraine that broke out after the annexation of Crimea that has cost the lives of some 10,000 people.