Prime Minister Imran Khan chaired a meeting of his senior cabinet members and close aides on Monday, to discuss the resolution passed by the European Parliament, which called for a review of their trade relations with Pakistan.
The European Parliament's resolution is linked with Pakistan's controversial blasphemy laws, and could potentially end Pakistan's eligibility for the Generalised Scheme of Preferences (GSP) trading status.
"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 him strong condemnation and objection," an EU spokesman told a news briefing.
The designation issued on Friday requires Meduza to label itself as such, subjecting it to increased government scrutiny.
"We reject the decision by the Russian authorities to include independent media outlet Meduza on the list of 'foreign agents'," a spokesman for EU foreign policy chief Josep Borrell, said in a statement.