The ministry has sent out a special letter to the country's universities, asking to be notified about planned events involving staff members of the EU Mission to Russia.
"Amid the deterioration of the relations with Russia due to the crisis in Ukraine, one of the tasks of the European Union in this phase is to spread its views of the Russian Federation's foreign policy course in the Russian society," reads the letter cited by the Russian newspaper, Izvestia.
According to the letter, Ušackas' agenda of visits indicates a focus on "regional work" by way of international programmes for university students and academic youth.
The Russian ministry issued a special warning in connection to the student exchange programme Erasmus for All, which it described as a tool for disseminating European propaganda and training activists to become supporters of EU policies in Russia.
The letter also emphasizes the need for thorough preparations for meetings with EU diplomats, saying that students should be briefed on Russia's official position regarding Crimea to "neutralize the EU position behind the sanctions on 'annexation of Crimea', as well as on violations of international law and 'other propaganda clichés'."
Asked to comment on the letter, representatives of four Russian universities said they understood and supported the ministry's fears. However, some said defending national interests may lead to total isolation, complete absence of meetings and communication with foreigners.
In an interview to Rossiya 24 television on Tuesday, Ušackas said that the EU currently sees no reasons for revoking the EU's sanctions on Russia but would want to normalize the relations with Russia.
"Unfortunately, we remain hostages to the conflict in Ukraine and the fact that Russia unlawfully annexed Crimea," said the Lithuanian diplomat.
"Efforts to isolate society"
EU Ambassador Ušackas says that dialogue must be maintained even during crisis, and the efforts to isolate the society from contacts with the outer world do not benefit anyone.
"The strength of any society is reflected by the way it manages diversity, pluralism, tolerance and remain open to dialogue. Attempts to isolate society from contact with the outside world benefits nobody," Ušackas told BNS on Wednesday.
The ambassador emphasized that the main function of the EU was to "to serve as a diplomatic channel of communication, maintain good contacts with the Russian government and represent the EU and its official positions."
"I am glad that even in times of most serious political tension we continue the dialogue on subjects of common interest and develop further relations in the fields which are not affected by restrictive measures (sanctions)," said Ušackas.
The diplomat said he was "committed to continue the outreach towards all voices of Russia: government officials, politicians as well as representatives of business, culture, science and education from different parts of Russia."
"During the acute crisis in our relations, we should talk and listen to each other with a view to understand each other better and to promote the bridges between our people. Сrisеs arrive and pass. The nations and states will remain and for that we need to talk, promote links and rebuild trust," said Ušackas.