Russian news agencies on Wednesday cited Constitutional Court chairman Valery Zorkin as saying the treaty signed by Putin has been ruled valid, thus formally clearing another hurdle for Moscow to annex Crimea. The treaty now only requires ratification by the Russian parliament.
A Ukrainian serviceman and a member of a militia were killed by gunfire in the incident in Crimea on Tuesday.
It is unclear whether the militiaman was a Ukrainian citizen. Although Moscow has insistently denied it has not deployed its own troops in Crimea, people in the peninsula have reported seeing a large number of military vehicles with Russian plates.
Thousands of troops under apparent Russian command took over Crimea two weeks before Sunday's hastily called referendum, seizing Ukrainian military bases, blockading others and pressuring Ukrainian soldiers to surrender their arms and leave.
Putin insisted Russia's military presence in Crimea was limited to those stationed under the terms of a treaty with Ukraine that allows Russia to have up to 25,000 troops at its Black Sea fleet base. Ukraine claims that Russia deployed further forces, however, and expressly went against its request for troops to remain confined within their barracks.
AP writer Peter Leonard contributed to this report from Kiev, Ukraine.