The two fishermen crossed the maritime border on Saturday and were later detained by authorities in the South. It is the first time South Korea
After crossing the border on their squid fishing boat, it took two days for the South Korean navy to seize the fleeing fisherman.
Ministry spokesperson Lee Sang-min said South Korea decided to expel the two men to North Korea because they were “heinous criminals”.
He added that they could not be recognised as refugees under international laws.
Mr Lee said the pair were sent back to North Korea.
According to the South Korean investigation, 19 people were aboard the fishing boat when it left the North’s Kimchaek port on its east coast in August.
While fishing in waters near Russia the two men collaborated with another crew member and killed the captain, ABC news reports.
The men claim they killed the captain because of his harsh treatment.
They then killed the other protesting crew members, one by one.
The bodies were dumped overboard.
The three men sailed back to Kimchaek port, North Korea, but after one man was arrested, the two fled using the same boat, the Unification Ministry said.
The vessel was chased by a South Korean navy ship, which fired warning shots at them.
After two days on the run, the pair were captured by the South Korean navy.
They later told investigators they wanted to resettle in South Korea, but South Korean authorities determined they only wanted to avoid North Korean arrest and on Tuesday informed North Korea of their planned deportation, the ministry said.
The unification ministry in Seoul told the BBC that “when we couldn’t trust their intention of defection” so they decided not to allow the “serious criminals” to stay.
The move to deport them is highly unusual, as South Korea has a policy of accepting North Koreans who want to resettle in the South to avoid political oppressions and poverty at home.
About 32,000 North Koreans have fled to the South since the end of the Korean War, at great personal risk.