Lavrov regretted what he called the lack of normality in relations between Moscow and Brussels, the two biggest actors in the Eurasian space.
It is definitely not a healthy situation which benefits no one, the Russian foreign minister said.
Relations between Russia and the EU have become strained over the alleged poisoning of Navalny by Russian secret service agents.
The outspoken critic of Russian President Vladimir Putin was arrested after returning to his homeland from Germany, where he was recovering from the suspected poisoning attack.
His detention last month has sparked a wave of protests across Russia and led to widespread condemnation from the international community.