They have called for him to publicly apologise and offer formal compensation.
They say unless this happens the leader should not be allowed to visit Seoul as expected this spring, following reconciliation efforts between North and South Korea.
"Kim Jong-il must be arrested and punished if he comes to Seoul without admitting his criminal acts and offering an apology and compensation," lawyer Lee Chul-sung, who leads a South Korean right-wing group, said after filing the lawsuit with the Seoul District Prosecutor's Office.
Agent's confession
Relatives allege that Mr Kim ordered the terrorist attack of KAL Flight 858 in 1987.
A female North Korean agent arrested soon after the attack told South Korean security officials that she was directly ordered to do so by Mr Kim.
The event led to North Korea being placed on the United States list of countries accused of supporting international terrorism.
The North has recently held several rounds of talks with US officials aimed at getting its name removed from the list which effectively blocks international financial institutions from giving loans to the impoverished state.
Reconciliation policy
Prosecution officials - who by law will study the claim before a decision to indict the North Korean leader is made - have said privately that an indictment was unrealistic and highly unlikely, reports said.
South Korean President Kim Dae-jung has espoused reconciliation with the North as a key policy of his three-year-old
government.
A coalition of conservative groups have also filed a letter of complaint to the prosecutors' office accusing the North Korean leader of involvement in other criminal incidents.
Among the incidents cited were the abduction of civilians and the bombing in the Burmese capital, Rangoon, in 1983 in which about 20 people were killed.
Those filing the petitions said that if their attempts to get justice failed, they would not give up but turn to the international criminal court in The Hague for help.