Iranian authorities on Saturday were still trying to determine the facts surrounding the incident which happened on Friday. It was not clear if the fishing boats had strayed into Saudi waters.
"Even if the boats had entered Saudi waters, the coastguards were not authorised to open fire," Majid Aghababaie, head of border affairs at Iran's interior minstry said.
"Two fishing boats were in the Persian Gulf and strayed due to high waves. The Saudi coastguards say the boats entered Saudi waters and killed one of the fishermen," Aghababaie said. One of the boats is still missing.
"We are pursuing this matter to determine if the Iranian boats had crossed the Saudi border or not, but the action of the Saudis does not comply with humanitarian and navigational principles," the Iranian minister said.
There was no immediate reaction from Saudi Arabia.
The incident comes amid rising tensions between the two Middle East nations.
Iran's Revolutionary Guard has accused Saudi Arabia of involvement in the attacks earlier this month on the parliament building and the shrine of revolutionary leader Ayatollah Ruhollah Khomeini in Tehran in which 17 people were killed. The so-called "Islamic State" group claimed responsibility for the attacks.
"Saudi Arabia is sponsoring terrorist groups in Iran," Iran's Intelligence Minister Mahmoud Alavi said on Thursday.
Iran and Qatar
Saudi Arabia, along with other Arab nations, cut diplomatic ties with Qatar last week over perceived ties to terrorist groups.
Iran's relationship with Qatar was also listed as one of the reasons for dropping the diplomatic links.
Iran sent planeloads of food to Qatar in a humanitarian gesture .
Iran and Saudi Arabia also support opposing sides in the conflicts in Syria and Yemen.
Iran and Saudi Arabia severed diplomatic ties in January 2016.
kbd/jm (AFP, AP, Reuters)