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".
The Saudi navy has captured three members of Iran's Revolutionary Guards from a boat seized last week as the vessel approached Saudi Arabia's offshore Marjan oilfield, Riyadh has said. "It was captured with the three men on board, the other two escaped", a statement from the ministry's center for worldwide communications said.
The official confirmed the three small boats, bearing red and white flags, entered the Saudi territorial waters in the Gulf.
Fishing is common enough in these waters, though Saudi Arabia's massive distrust of Iran and the incident's proximity to a lucrative off-shore oil field appears to be tailor-made for the Saudis to interpret the incursion as some broader plot against them.
The statement, however, did not say who was behind the attack.
One of the boats was intercepted, while the two others managed to get away.
The Foreign Ministry spokesman said the Saudi coast guard's move to shoot and kill an Iranian fisherman was illegal and devoid of any justification.
Saudi Arabia, the United Arab Emirates, Egypt and others severed diplomatic and economic ties with Qatar two weeks ago, accusing Doha of supporting groups, including some backed by Iran, "that aim to destabilise the region".
On Sunday Iran fired missiles into Syria, claiming it was hitting Islamic State targets in retaliation.
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.