The suspected hijacking of a fishing vessel carrying South Koreans in the Indian Ocean on Saturday turned out to be a false alarm, Seoul's foreign ministry said.

The ministry said earlier that a 234-ton Mongolian-flagged squid fishing vessel was apparently hijacked by what was thought to be a pirate ship in waters 1,400 kilometers southeast of Salalah, Oman, at around 12:20 a.m. Saturday (Seoul time). 

The ship that departed from Indonesia heading to Oman carries three South Koreans and 18 Indonesians. Before it went missing, the crew sent a dispatch that a suspected pirate ship was trailing them.

"We confirmed the safety of the three South Korean crew members after the company of the vessel's local partner got in contact with the captain at 5:23 p.m.," a ministry official said.

The official said that the South Korean Embassy in South Africa also contacted the headquarters of the ship's company in the African nation and confirmed the safety of the crew.

The cause of the 17-hour communication loss hasn't been confirmed.

Another ministry official confirmed that the incident was not a hijacking but said it appears that the vessel chased off another ship that was suspected to be run by pirates.

The ministry is in the process of getting an accurate account of what occurred.

President Moon Jae-in earlier in the day directed the government to make all-out efforts to rescue the sailors, who were then believed to have been kidnapped.

The military had deployed the Cheonghae Unit, a South Korean naval contingent, to the scene to initiate a rescue operation of the ship then believed to have been hijacked.

The Cheonghae Unit has been manning a 4,500-ton destroyer in the Gulf of Aden since 2009 as part of global efforts to combat piracy off the coast of Somalia.

In 2012, Navy commandos from the unit raided a South Korean freighter that had been hijacked by Somali pirates in the Arabian Sea, rescuing all 21 crew members and killing eight pirates. (Yonhap)