A US official reportedly said that Israel had informed Washington it had struck the vessel in "retaliation for earlier Iranian strikes on Israeli vessels".
Iran's foreign ministry has said that an Iranian vessel, the Saviz, had been targeted in the Red Sea, a day after media reports that the ship had been attacked with limpet mines.
"The explosion occurred on Tuesday morning near the Djibouti coast and caused minor damage with no casualties. The vessel was a civilian ship stationed there to secure the region against pirates," Foreign Ministry spokesman Saeed Khatibzadeh said.
"The issue is under investigation".
It was the latest in a reported series of attacks on Israeli- and Iranian-owned cargo ships since late February in which the two arch-enemies accused each other of responsibility.
'US did not carry out the attack'
The incidents have occurred since US President Joe Biden took office in January with a commitment to rejoin world powers' 2015 nuclear deal with Iran - abandoned by his predecessor Donald Trump in a move welcomed by Israel – if Tehran returns to full compliance with the deal.
Iran and the United States on Tuesday launched indirect talks in Vienna that included the other powers on ways to revive the deal. Both Iran and the United States called the talks "constructive."
US officials, who spoke on the condition of anonymity on Tuesday, told Reuters that the United States did not carry out an attack on an Iranian vessel.
Meanwhile, The New York Times cited a US official as saying Israel had informed Washington it had struck the vessel in "retaliation for earlier Iranian strikes on Israeli vessels".
Israel silent on the incident
Israeli officials declined comment on Tuesday's reported attack on the Iranian cargo ship.
Earlier in the day, before news broke about the attack, Israeli Prime Minister Benjamin Netanyahu, in comments to lawmakers of his right-wing Likud party, said there should be no return to the "dangerous" nuclear accord and added:
"In parallel we must continue to fend off Iranian belligerence in our region. And this threat is no theoretical matter. I'm not uttering it rhetorically. We must take action in the face of the fanatical regime in Iran, which simply threatens to wipe us off the face of the earth."
The Biden administration is not anticipating any changes on Iran policy amid the negotiations over reinstating the nuclear deal, White House spokeswoman Jen Psaki said on Tuesday.
There have been three other reported attacks on Iranian- or Israeli-owned shipping since February 25.
On March 25 a cargo ship owned by an Israeli company was damaged by a missile in the Arabian Sea in what was suspected to be an Iranian attack, according to a senior Israeli security official. The ship was able to continue its journey, he said.
Two weeks before, Iranian state media quoted an Iranian investigator as saying Israel was highly likely to have been behind an explosion that caused a small fire on an Iranian container ship in the Mediterranean.
Israeli Defence Minister Benny Gantz declined to comment directly at the time but said Iran regularly sent weapons to its proxies in the region.
On February 26, Netanyahu blamed Iran for an explosion aboard an Israeli-owned vehicle-carrier ship in the Gulf of Oman.
A US official said the blast ripped holes in both sides of its hull and an Israeli official said limpet mines were used. Iran denied responsibility.