Aghababie said on Monday that a Saudi claim the boats entered the kingdom's waters had not been proven.
"The three captured members of the Iranian Revolutionary Guards are now being questioned by Saudi authorities", it said, citing a Saudi official. "It was captured with the three men on board, the other two escaped", a statement from the ministry's center for worldwide communications said. Their destination was the Marjan oil field, it said.
That statement made no mention of explosives and did not detail what type of weapons were found, though it said they were for "subversive purposes".
In April, Saudi security forces said they thwarted an attempted attack on an oil distribution center involving an unmanned boat from Yemen loaded with explosives.
North Korea releases detained U.S. student: How is he doing?
He said officials had counseled the family to not speak out about Otto's detention, to avoid antagonizing the North Korean regime. His family asked his doctors to disclose details about his condition amid intense scrutiny and questions about his condition.
The assault was not only aimed at sending a message to IS, but also to the USA and Saudi Arabia.Tehran had repeatedly accused the Saudis and Washington of supporting terrorists and trying to destabilize Iran.
On Saturday, Iran accused the Saudi coastguard of killing one of its fishermen after two fishing boats may have strayed into Saudi waters. After Islamic State suicide bombers attacked key landmarks in Tehran - including parliament - on June 7, the Guards issued a statement with barely veiled references to a Saudi role in the carnage. "When Iran looks at ISIS it sees Saudi Arabia".
In Iran, the Interior Ministry director general for border affairs, Majid Aqababai, said "Saudi Arabia's claim on the arrest of Iranian military personnel is not true because the individuals who were confronted were simple fishermen on a fishing boat".