When North Korean soldiers found a South Korean fisheries official in their territorial waters, they shot him dead and burned the body -- an incident so shocking it later prompted Kim Jong Un to apologise.

Details are sketchy -- and mostly classified -- but exactly how and why the official came to be floating in a life jacket above the sea border known as the Northern Limit Line in September 2020 has become a bitter political debate in the South.

Was the 47-year-old official, Lee Dae-jun, a would-be defector fleeing gambling debts, as the government of then-president Moon Jae-in said citing intelligence it then sealed for 30 years?

Or is that version of events actually a high-level smear campaign and cover-up, as the new government of Yoon Suk-yeol has claimed in raiding an ex-spy master's house and launching legal action over the former administration's handling of the case?

The intelligence services claim that their former chief, Park Jie-won, destroyed evidence showing Lee had no plans to move to Pyongyang.

Park told AFP the charges were "political revenge on the former administration", dismissing the allegations as unfounded.

Seoul's new administration has also reopened enquiries into a second explosive case, in which two North Korean fishermen who confessed to killing 16 crewmates at sea were deported in 2019.

Dramatic video showing the pair being dragged seemingly unwillingly through the heavily fortified Demilitarized Zone (DMZ) and returned to the North was released by Yoon's conservative government.

Moon's government at the time said the brutal nature of the killings meant the men were not entitled to the usual protections afforded to North Korean defectors and could not be considered refugees.

The political fight over the two cases highlights the risks of interpreting classified intelligence and the law in highly partisan ways, analysts say.

Critics argue the hawkish Yoon, who is struggling with record-low approval ratings just months after becoming president, is engaging in old-school red-baiting in a bid to salvage his popularity with disgruntled voters.

"For conservatives, these two cases are an example of liberals taking a subservient approach to the North," lawyer and columnist Yoo Jung-hoon told AFP.

But "the timing of the probe that came right after the change of power raises questions of a political motive behind it," he added.

Supporters of Yoon, a former prosecutor who won a close election in March vowing to get tough on Pyongyang after years of failed diplomacy, say he is simply trying to solve the cases.

"It would be a bigger problem if prosecutors chose to ignore the allegations and bury the cases fearing it would be called a 'political investigation'," Shin Yul, a professor at Myongji University, told AFP.

Legal experts say the cases have exposed contradictions in the country's constitution.

Trying the fishermen in South Korean courts would have been unprecedented, as it was unclear whether local courts had jurisdiction.

One clause of South Korea's constitution describes the country's territory as "the Korean peninsula".

Yoon has suggested that clause meant the men should have been considered South Korean citizens and tried at home.

But the next clause pledges to work for "peaceful reunification" with the North, recognising the reality that there are two distinct countries on the peninsula.

"Seoul has to take a realistic approach when dealing with the North," said Kim Jong-dae of the Yonsei Institute for North Korean Studies.

Yoon's administration has accused Moon's government of sending the fishermen "straight to death row" by repatriating them to the North.

But critics say the president has prioritised "revenge politics" over dealing with more pressing policy issues such as spiralling inflation and a plunging currency.

Seeking to prosecute officials while not presenting "smoking gun" counter-evidence in either case looks suspicious, said Kim Jong-dae.

"The administration is charging ahead with punitive governance with prosecutors on the forefront," he said.

"It's one thing to raise questions and demand answers about how the former government handled the two cases. But investigating ex-officials is a totally different thing that inevitably raises suspicions of political motives."