Deputy General Director Eduard Kuznetsov said the agency will continue using an early-warning attack station based in Sevastopol, Crimea, but would close the Mukachevo facility following Moscow's decision to stop using it.
Russia terminated an agreement on the use of both radars (Sevastopol and Mukachevo) in February 2008 on the grounds that they are operationally obsolete. Kiev called Moscow's move unfriendly.
The two radar facilities allow Ukraine to track missile launches at a distance of up to 1,500 kilometers.
Kiev has not ruled out that once the radars are no longer used by Russia that they could be used "in the interest of EU countries."
Moscow has strongly opposed the possible deployment by the U.S. of 10 interceptor missiles in Poland and an accompanying tracking radar in the Czech Republic as a threat to its national security.
The Kremlin has also expressed concern over NATO's expansion to Russia's borders and pledged to take "appropriate measures."