"Discussions on the issue have been held, and Khabarovsk has been selected," Sergei Prikhodko said.
Khabarovsk was chosen ahead of Kazan, the capital of Russia's Volga republic of Tatarstan.
The Czech Ambassador to Russia, Miroslav Kostelka, whose country holds the rotating EU presidency, earlier said the summit was scheduled for May 21-22.
The EU and Russia hold summits every six months. Russia traditionally hosts the event in the first half of the year, and the country holding the rotating EU presidency acts as the host in the second half.
Moscow has hosted five such summits over the past nine years. The previous Russian venue for the summit was Khanty-Mansiisk in West Siberia.
Meanwhile, Russia's south Urals city of Yekaterinburg is currently completing preparations to host Shanghai Cooperation Organization (SCO) and BRIC summits in June.
"As concerns Yekaterinburg, there are no questions whatsoever," Prikhodko said, adding that the summits would be held in a "worthy and well-organized" manner.
The SCO regional security group comprises Russia, China, Kazakhstan, Tajikistan, Kyrgyzstan, and Uzbekistan. Iran, India, Mongolia and Pakistan have observer status. Russia took over the presidency of the organization last August.
The BRIC nations are Brazil, Russia, India and China.
