The ministry said in a statement that elite Underwater Defense (SAS) teams were dispatched to the area where the mine was found off the coast of Kefken, a small town in the district of Izmit, by a Liberian-flagged cargo ship.
The statement also said a security perimeter was established in the area.
Ukraine and Russia have accused each other of laying mines in the Black Sea, and in late March, Turkish and Romanian military diving teams defused stray mines around their waters.
Maritime officials say the risk of coming across floating mines in the major Black Sea shipping route is adding to perils for merchant ships sailing in the region, and governments must ensure safe passage to keep supply chains running.