The official news agency IRNA reported on Sunday that "a Qatari boat attacked an Iranian boat in the Persian Gulf, resulting in the killing and injuring of a number of crew members".
A top Interior Ministry official, Ali Asgar Ahmadi, said the fishermen were working near the small Iranian island of Lavan when they were attacked in the early hours of Friday.
"They were attacked by a Qatari naval boat. One fisherman was killed and two were injured. The boat was confiscated and the fishermen arrested," the deputy interior minister in charge of security affairs said.
"What has happened is unacceptable and not compatible with international rules and regulations. Iran will defend the right of Iranians," he added, calling for their immediate release and compensation to be paid.
The Iranian Foreign Ministry statement said Qatari ambassador Saleh Ibrahim al-Quwari was delivered a "strong protest" on Saturday, and told to ensure the boat and crew were immediately returned to Iran.
"Iran also wants those responsible to be identified and prosecuted," the ministry said.
According to IRNA, the Qatari ambassador to Tehran said he has "no information on the matter" but "will inform the officials concerned and will respond immediately".
"What has happened
is unacceptable and
not compatible with international rules and regulations. Iran will defend the right
Ali Asgar Ahmadi,
Iranian Interior Ministry official
When contacted by AFP news agency, the Qatari embassy in Tehran refused to comment.
The spat comes just a week after Iran protested to the United Arab Emirates, which it accused of firing on an Iranian boat and arresting its crew who were fishing in waters off a disputed Gulf island.
The Foreign Ministry complained over the "unacceptable" behaviour of the UAE, but an IRNA report later said the Iranian crew had been tired and had drifted into waters off Dubai.