The five ships are carrying a total of 21 Korean crew members, with one of them bound for South Korea, according to the ministry.
A total of 87 Korean nationals remain aboard vessels inside the strait, including 33 serving on foreign-operated ships.
The departures come as vessels gradually resume passage following an agreement between the United States and Iran to end the Middle East war.
The ministry said it would continue working with the Foreign Ministry, overseas diplomatic missions and relevant countries to ensure the prompt and safe passage of the remaining Korean vessels.
However, the reopening of the strait may not lead to an immediate return to normal shipping, as many tankers stranded in the Persian Gulf for months are facing another obstacle: marine growth accumulated on their hulls.
Barnacles, mussels and seaweed attached to the vessels can significantly reduce fuel efficiency and, in severe cases, damage propellers, according to a CNN report.
Large tankers must undergo professional underwater cleaning before resuming normal operations. A very large crude carrier may have about 14,000 square meters of underwater hull surface to clean, with a team of five or six divers taking four to five hours to service one vessel.
With about 600 tankers reportedly waiting in the region, limited cleaning capacity could create another bottleneck and delay departures. The cost of underwater hull cleaning has also risen to tens of thousands of dollars per vessel amid surging demand.
The developments suggest that while traffic through the Strait of Hormuz is gradually resuming, restoring the global energy supply chain may take considerably longer.
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