"The government made a decision to expel them as they had committed grave, non-political crimes such as murder and were not subject to our protection under the law", ministry spokesman Lee said.
South Korea deported two North Koreans back to the communist nation after learning that they killed 16 fellow crew members on their fishing boat and fled to the South, the unification ministry said Thursday.
"The government has chose to deport them as they have committed a heinous crime".
The diplomat blamed the joint aerial drills - which Pyongyang views as a rehearsal for an invasion - for "throwing cold water" over talks with Washington.
But when they arrived at the North's Kimchaek port last week, with the intention of a quick turnaround, the third man was detained and the pair fled south in the same boat.
As violent criminals, the two would not be recognized as refugees by worldwide law, Lee said.
North Korean official Kwon Jong Gun on Thursday accused the USA of trying to resume joint aerial drills with South Korea next month, AP reported.
North Korea still carries out public executions, including by firing squad and hanging.
The Coast Guard rescued 60 North Koreans but there was no way to confirm they had been illegally fishing within Japan's exclusive economic zone (EEZ) - as their boat had sunk. Acting out of anger against the abusive skipper, the three accused killed him and murdered the remaining 15 to cover up their first crime, according to the minister.
They were chased by a South Korean navy ship which fired warning shots at them.
A North Korean defector said it was "absolutely certain" that the two will be executed in the North.
Aside from the accusations of murder, the case is unusual in that it is the first time Seoul has returned any North Koreans trying to flee the nation since the Korean War, which ended in 1953, according to the Associated Press.
The government has also planned to send back the fishing boat of the North Koreans, Lee added.
About 32,000 North Koreans have fled to the South since the end of the Korean War, majority via China and in the past two decades. South Korean officials told the Yonhap News Agency the drills will be conducted at a smaller scale compared with previous years.