"The Russian ambassador has been summoned, he should be received in the afternoon by the secretary general of the European Commission and of the European External Action Service, where we will convey to him strong condemnation and objection," EU spokesman Peter Stano told a news briefing.
"There is no legal explanation whatsoever for such an action ... the Russian decisions in this regard, all these counter-sanctions, are obviously very politically motivated and lack any legal justification," Stano said.
Russia's foreign ministry said on 30 April those banned included Vera Jourova, vice president for values and transparency at the executive European Commission, David Sassoli, the president of the European parliament, and Jacques Maire, a member of the French delegation at the Council of Europe's Parliamentary Assembly.
The EU will consider its next steps at a meeting of foreign ministers next week but may also look to the Council of Europe, a non-EU body of which Russia is a member, for ways to respond to what Brussels says are continued Russian rights abuses.
Moscow has called on the EU not to interfere in its internal affairs and denies any wrongdoing.
Navalny recovered in Germany from an attack with nerve agent last year and was detained upon his return to Russia in January. He was sentenced in February to 2-1/2 years in prison for parole violations on an earlier embezzlement conviction that he says was politically motivated.
Navalny blamed the attack on Putin. Russian authorities denied any involvement and questioned whether he was even poisoned.
The EU imposed sanctions in March on two Russians accused of persecuting gay and lesbian people in the southern Russian region of Chechnya. The EU also imposed sanctions on four senior Russian officials close to President Vladimir Putin in March.