An Iranian military support ship linked to the Islamic Revolutionary Guard Corps was attacked in the Red Sea, the country's Foreign Ministry confirmed on Wednesday.
While the Saviz is officially listed as a commercial vessel, it has been referred to as a "mother ship" of the IRGC's navy.
It was described in a report by the Washington Institute for Near East Policy think tank as a spy ship disguised as a cargo ship.
"The Saviz was slightly damaged in an explosion in the Red Sea off the coast of Djibouti on Tuesday, April 6, at around 6am local time," Saeed Khatibzadeh, spokesman for the Iranian foreign ministry, said on Wednesday.
Mr Khatibzadeh said investigations were under way into how the incident happened and its origin.
Iran, he said, had informed the International Maritime Organisation to begin investigations.
On Tuesday evening, the IRGC-linked Tasnim news agency said limpet mines were used in the attack.
"The vessel Iran Saviz has been stationed in the Red Sea for the past few years to support Iranian commandos sent on commercial vessel (anti-piracy) escort missions," it reported.
US Central Command, which maintains forces in the area, was not involved in the incident but was aware of reports of the attack, said spokeswoman Erin Dorrance.
The New York Times reported a claim from a US official that Israel had notified the US that its forces struck the vessel about 7.30am local time.
The report said the attack was retaliation for previous strikes and that the Saviz was damaged below the waterline.
Munro Anderson, a partner for security company Dryad Global, said the incident could be a response to the attack on Israeli vessel MV Lori in the Arabian Sea on March 25.
Israel also blamed Iran for sabotaging a commercial vessel, the Helios Ray, which was damaged by limpet mines on February 28.
Last month, Iran accused Israel of a sabotage campaign against its vessels, including oil tankers.
IRGC commandos are accused of operations against oil cargoes at sea and anchored in port, after the administration of former US president Donald Trump imposed tough sanctions in 2018 and Washington withdrew from the 2015 nuclear deal.
Despite the chance of easing tensions between Washington and Tehran under the administration of President Joe Biden, the apparent sabotage campaign continued.
On Tuesday, European mediators began constructive indirect talks between the US and Iran in Vienna on reviving the nuclear deal.
Neither the US nor Iran are expecting swift breakthroughs. Tehran demands Washington drop sanctions before it returns to compliance with the 2015 nuclear deal and Mr Biden's administration demands that Iran reduce enrichment to agreed levels before it will consider dropping Mr Trump's sanctions.
What is the 'Saviz'?
According to analysis by the US Naval Institute, the Saviz is intended to look like an ordinary commercial vessel.
But analysts said the ship carries speedboats similar to those used by the IRGC's naval arm, the institute said.
The ship is reportedly anchored for long periods near southern Yemen in the Bab Al Mandeb, one of the world's busiest shipping routes.
"Automated information system transmissions and analysis of commercial satellite images show the ship has barely moved in the past three years," the institute said.
"From its position, the ship can provide constant surveillance of maritime traffic."