Ukrainian President Viktor Yushchenko signed the decree Wednesday stating that Russia was required to notify the Ukrainian authorities of all movements by naval vessels and aircraft from its Crimea-based Black Sea Fleet.
"The new directives are aimed at creating a serious obstacle for the day-to-day operations of the Fleet and contradict the 1997 agreements between Russia and Ukraine on the status and terms of the Russian Black Sea Fleet's presence on Ukrainian territory," the ministry said in a statement.
According to the decree, Russia must seek permission from Kiev for the movement of its warships and aircraft beyond Ukrainian borders. Permission is to be sought no later than 72 hours prior to any planned maneuvers.
"This unilateral step delivers another blow to talks on the issue of the Black Sea Fleet as well as the whole range of bilateral relations," the statement said.
The ministry also said "Russia regards the Ukrainian leader's actions as contradicting the spirit and letter of the named agreements and the 1997 Agreement on Friendship, Cooperation and Partnership between the Russian Federation and Ukraine."
Ships from Russia's Black Sea Fleet patrolled the waters off the Georgian coast during Russia's "peace enforcement" operation that began after Georgia launched an offensive in breakaway South Ossetia on August 8.
Yushchenko signed the document after returning from Tbilisi, where he took part in a mass rally in support of Georgian President Mikheil Saakashvili amid fighting with Russia. Both leaders have pursued pro-Western policies, seeking to join NATO and the European Union and reduce Russian influence.
Russia's Black Sea Fleet uses the Sevastopol base under an agreement signed in 1997. Yushchenko announced earlier this year that Ukraine would not extend the lease beyond 2017.
In early June, Russia's lower house of parliament adopted a resolution saying the Russian-Ukrainian cooperation treaty could be declared invalid if Ukraine joins NATO.
Ukraine's pro-Western leadership has been pursuing NATO membership since Yushchenko's 2004 election. Ukraine failed to secure an agreement on a NATO Membership Action Plan, a key step toward joining the alliance, at the organization's summit in April, but was told the decision would be reviewed in December.