The move to return the ships would be ahead of a four-way summit on eastern Ukraine next month.
A Reuters reporter in Crimea saw tug boats pulling the three vessels through the Kerch Strait towards the Black Sea where they could potentially travel onwards towards Ukraine.
Russia seized the ships off the coast of Crimea in November last year after opening fire on them and wounding several sailors.
Moscow said the ships - two small Ukrainian armored artillery vessels and a tug boat - had illegally entered its territorial waters. Kiev denied that.