The decision has left local fans of the superstar fuming.
LPF chairman Abdul Halim Abdul Hamid saidthe board had requested the makers for the alterations in the movie, so that the the viewers continue respecting the law.
"Normally under our guidelines, there must be some kind of element of retribution in the movie. Especially if the characters shown in the movies are involved in crime, then there must be some kind of comeuppance for that.
The film ran to full shows yesterday with fans queuing up hours before the show.
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Set in Malaysia, the movie features Rajinikanth as a gangster, who was framed for a crime decades ago.
The original ending scene in the movie was intentionally left ambiguous, but the local version leaves nothing to the audience's imagination.
Abdul Halim also admitted that the board had censored several scenes in the Kollywood film, but stressed that all the cuts were only five minutes in total and that the storyline of the movie was still intact.
"We have our own guidelines and anything that we feel could be sensitive, we censor. We took off the word and it's better that way because if we do not do that, then the people will allege that we practice selective censorship."
The scene in the original unedited version has since been slammed in Malay paperMingguan Malaysiatoday. An article had accused the film of deliberately flaming racial tensions in the country by portraying the ethnic Indians as an oppressed minority.
Despite that, Abdul Halim said the main reason for the censorship was to make the movie a PG-13-rated film, so it could be seen by more Malaysians.
Eight percent of multi ethnic Muslim majority of Malaysia's population is Indian, mostly Tamil.