The blast struck the Iranian commercial vessel MV Saviz off the coast of Djibouti on Tuesday morning, Foreign Ministry spokesman Saeed Khatibzadeh said, adding an inquiry had been opened into the cause.
"The accident caused no casualties and a technical investigation is under way to determine its circumstances and origin," the spokesman said, according to AFP.
"Our country will take all necessary steps through international bodies in this regard."
Khatibzadeh said the Saviz was a civilian vessel that had been deployed in coordination with the International Maritime Organization to protect shipping in the Red Sea and the Gulf of Aden.
Many foreign governments have stationed protection vessels in the area since a rash of attacks by Somali pirates between 2000 and 2010.
"This ship has been serving as Iran's logistics station – for technical and logistical support – in the Red Sea," the spokesman added.
Overnight, Tasnim News Agency reported that the Saviz had been damaged by magnetic mines.
The Iranian media outlet said the ship had been stationed in the Red Sea for several years "in support of Iranian commandos deployed to escort commercial vessels".
According to specialist website, MarineTraffic, the Saviz is a general cargo ship owned by Iran's state shipping firm IRISL.
In a similar incident last month, an Iranian cargo ship was damaged after it was targeted in an attack en route to Europe in the Mediterranean Sea.
Tehran said back then that such “acts of terror” are a clear example of naval piracy and run counter to international law on the safety of commercial vessels, Press TV wrote.
On February 25, an explosion struck Israeli-owned and the Bahamas-flagged ship, the MV Helios Ray, in the Sea of Oman near the strategic mouth of the Persian Gulf.
Israeli Prime Minister Benjamin Netanyahu accused Iran of attacking the ship. Iran categorically rejected the charge.
Iranian Ambassador to the United Nations Majid Takht-Ravanchi, in a letter addressed to UN Secretary-General Antonio Guterres on March 5, warned of consequences of any possible miscalculated measure by Israel over the explosion.
“The incident has all the characteristic of a complicated false flag operation carried out by actors in order to pursue their malign policies and to advance their illegitimate objectives,” Takht-Ravanchi said.