Kim, 57, is one of South Korea's top directors whose awards include the Golden Lion at the Venice Film Festival for "Pieta" in 2012.
But an actress last year accused him of sexual and physical abuse, saying he forced her into unwanted, unscripted sex and nude scenes and slapped her repeatedly while shooting his 2013 award-winning film "Moebius" -- before replacing her with another actress.
Prosecutors dropped the sex abuse charge citing lack of evidence but fined Kim five million won ($4,600) for assault under a procedure to settle minor cases out of court.
The actress - who said she had quit acting due to trauma - has appealed against the decision to dismiss the sex abuse allegation.
Kim admitted slapping her as part of "acting lessons". His latest work "Human, Space, Time and Human" will have its world premiere in the Panorama Special section of this year's Berlinale, which begins Thursday.
"We are living in this unfair reality in which a physical assault offender is working and being welcomed everywhere as if nothing happened, while the victim who spoke out against the abuse is being isolated and marginalised,"
the alliance of about 140 civic groups said in a joint statement sent to AFP.
The organisations -- including major South Korean women's rights and human rights groups, NGOs helping sex abuse victims and various filmmakers' associations -- earlier voiced support for the actress.
Berlinale chief Dieter Kosslick has said this year's festival would serve as a "forum" to discuss ways to combat abuse of women in the film industry.
He also said the organisers had disqualified some works involving individuals accused of credible sex abuse allegations from this year's event.
"Then why is the Berlinale offering an indulgence to Kim by rolling out a red carpet to him and his movie?" said the statement, referring to the Roman Catholic practice of eliminating or reducing punishments for sins.
The coalition accused the Berlinale organisers of "condoning and endorsing" Kim's actions.
It noted that Kim's victim was assaulted on a film set, like many actresses "with little experience, little recognition in the industry, or little power" who "suffered various forms of violence at the hands of powerful figures".
Her allegation is a rarity in South Korea's male-dominated and tight-knit film industry, where those who speak out against abuse by a director or a producer risk being banned from the industry for good.
Berlinale organisers noted that the sex abuse allegation was dismissed but said the festival "opposes and condemns any form of violence or sexual misconduct".
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