"We have nothing to report in relation to this tragedy because the ship that sank on Saturday near the Bulgarian coast belongs to North Korea...The crew was not Russian either," the ministry said in a statement.
The Bulgarian Ministry of Transport earlier reported that the Russian Tolstoy cargo vessel with 13-member crew on board sank about 04.00 local time 10-15 miles off the Bulgarian coast.
Russian officials said the Bulgarian authorities had apparently mistaken the nationality of the ship because of its name, which refers to the famous Russian writer Leo Tolstoy, the author of War and Peace.
Meanwhile, Bulgaria's Darik Radio said sea search-and-rescue teams, including a Bulgarian military helicopter, are attempting to find the survivors, but the rescue operation is hampered by bad weather.
A Bulgarian Navy frigate is expected to join the rescue effort later on Sunday.
Darik Radio said the 138-meter-long cargo vessel was carrying scrap metal from Rostov-on-Don in Russia to Nemrut in Turkey.
The ship has reportedly been in service for 37 years and was recently cited for numerous technical problems.