Two other boats that also approached Marjan managed to escape after the Saudi navy fired warning shots, the agency reported. The three "are now being questioned by Saudi authorities", the information and culture ministry said in a statement, at a time of already-heightened tensions with Iran.
On Friday, Iran accused Saudi coast guards of opening fire on Iranian fishing boats, killing a fisherman. "They are from Bushehr and were fishing when they were arrested by the Saudi coastguard", said Aghababaie.
The vessel, which was seized last Friday, was carrying explosives and the those captured meant to conduct a "terrorist act" in Saudi territorial waters, it claimed.
"There is no proof that they are military personnel", he said, in remarks carried by the ILNA news agency.
Saudi Arabia regularly accuses Shiite-dominated Iran of interfering in Middle Eastern countries, and has suggested it is linked to instability in the kingdom's east, where minority Shiites live.
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Deputy Attorney General Rod Rosenstein talks to an aide on Capitol Hill on Tuesday while testifying before Congress. Susan Collins, R-Maine, said it would be "extraordinarily unwise".
"This Saudi move is not compatible with human principles and even assuming that the boats had crossed Saudi borders due to sea waves, they were not authorized to shoot at the Iranian boats", Tasnim news agency quoted Iran's Interior Ministry's Director General for Border Affairs Majid Aqa Babaei as saying.
"On Friday, 16th June, three small boats, bearing red and white flags, entered the Saudi territorial waters in the Arabian Gulf".
On Sunday Iran fired missiles into Syria, claiming it was hitting Islamic State targets in retaliation.
Saudi Arabia said Monday it had disrupted an attack on an offshore oil field.
Saudi Arabia on Monday said the three suspects it captured were Guard members aboard a boat heading to an oil platform in the Gulf, which separates the two rival nations.
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