Josep Borrell condemned Russia's move to expel European diplomats on Friday in an interview with Euronews.
The EU's top diplomat said that he learned of the news during his meeting with Russia's foreign minister Sergey Lavrov in Moscow.
"During my meeting with Minister Lavrov I got news that three European diplomats were going to be expelled," Borrell said.
"I strongly reject the decision. I reject the allegations that these diplomats were performing activities incompatible with their role as diplomats."
Russia's foreign ministry said it expelled diplomats from Germany, Poland and Sweden because they took part in illegal demonstrations in support of Alexei Navalny.
Tens of thousands of Russians protested last weekend in support of the Kremlin critic who was detained upon returning to Russia from Germany after recovering from being poisoned.
While Borrell said that EU-Russia relations are at their lowest level, the bloc is not planning on issuing sanctions.
"For the time being there is no proposal but things can change, let’s see next week," Borrell told Euronews. "This can be considered; nothing is excluded."