Yushchenko said he had presented Russia with "an urgent proposition to launch talks and draw up an agreement to regulate bilateral relations during military operations" such as those in Georgia over the past week.
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 a 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.
He 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.
Ukraine even threatened last weekend to refuse to allow the Russian vessels to return to the Sevastopol naval base. Russia's Defense Ministry said Sunday that the Russian Navy had sunk a Georgian vessel transporting missile launchers.
Russia's Black Sea Fleet uses the Sevastopol base under agreements signed in 1997. Yushchenko announced earlier this year that Ukraine would not extend the lease beyond 2017.