A Vietnamese coast guard vessel on Sunday reportedly intercepted an Indonesian maritime security patrol craft that was escorting five Vietnamese fishing boats that had been caught poaching earlier in the day.

Indonesia's Ministry of Marine Affairs and Fisheries said yesterday that the Vietnamese fishing boats were stopped in Indonesian waters near the Natuna Islands in the South China Sea.

But Vietnam claims the fishermen were in its own waters during the incident.

The clash on Sunday not only led to the Indonesian authorities losing custody of all five Vietnam-flagged boats it had detained, but also resulted in one of its own maritime enforcement officers being held by the Vietnamese coast guard.

The incident came just two days after Indonesian President Joko Widodo was in the Natunas to witness a major military exercise that involved more than 5,000 armed forces personnel.

In a similar confrontation in March last year, a Chinese coast guard vessel intervened in the same manner and freed a Chinese fishing boat, KM Kway Fey, after it had been held by an Indonesian patrol vessel. Jakarta later summoned the Chinese envoy to explain the Chinese coast guard's actions.

Indonesia and Vietnam, however, will resolve the matter amicably through diplomatic channels, said Ministry of Marine Affairs and Fisheries secretary-general Rifky Effendi Hardijanto at a press conference in Jakarta yesterday.

The Indonesian official added that he had met Vietnamese Ambassador to Indonesia Hoang Anh Tuan earlier to address the matter and agreed that they "will not fight at sea".

The five fishing boats were stopped by the Indonesian patrol on Sunday between 10am and 11.20am (local time), after they were spotted poaching in Indonesia's exclusive economic zone (EEZ) just off the Natunas, said Mr Rifky.

An EEZ is a zone extending 200 nautical miles from shore over which a state has rights regarding the exploration and use of marine resources under the United Nations Convention on the Law of the Sea.

As the Vietnamese poachers were being escorted to land for processing by officers from the Maritime and Fisheries Resources Monitoring Directorate-General, Mr Rifky said, a Vietnamese coast guard vessel showed up to obstruct their path at sea.

It would later be joined by three more Vietnamese coast guard vessels, according to the Indonesian patrol craft's log, seen by The Straits Times on Monday.

The log indicated that one of the Vietnamese coast guard vessels suddenly rammed against one of the fishing boats at about 1.10pm, effectively sinking it.

In the process, the Vietnamese took an Indonesian maritime enforcement officer, identified as Mr D. Gunawan Wibisono, hostage and demanded the release of the remaining four fishing boats and all 55 crew members in exchange.

The Indonesians complied as they were outnumbered, and allowed the four fishing boats and their crew to go free, but held on to 11 other Vietnamese fishermen.

Mr Rifky downplayed the element of hostage-taking, saying that although Mr Gunawan was still being held, he would be released soon.

Beijing's claimed territorial waters in the South China Sea, marked out by its nine-dash-line map, overlap with areas claimed by Brunei, the Philippines, Vietnam, Malaysia and Taiwan, resulting in territorial disputes.

Indonesia was never a party to the disputes, but was dragged into a similar territorial fracas with China after Beijing said in March last year during the KM Kway Fey incident that the waters in Indonesia's EEZ were in its "traditional fishing grounds".