"Undoubtedly what Salman said is wrong, the simile, example and the context. The intention was not wrong," Salim Khan tweeted on Tuesday.
"Nevertheless I apologise on behalf of his family, his fans and his friends. Forgiveness is to pardon the unpardonable or it is no virtue at all," added the 80-year-old veteran, who has in the past also come forward in his son's defence.
The screenwriter also said that on International Yoga Day, "let's not run our shops on this mistake".
Salman courted controversy after comparing himself to a 'raped woman' when he was asked to comment on his experience of shooting for his forthcoming film 'Sultan'. This happened during a media interaction in Mumbai on Saturday.
When Salman was asked how difficult it was to shoot wrestling scenes for the movie, he said, "While shooting during those six hours, there was so much of lifting and thrusting that it was unbelievable. If I was lifting a 120 kg person and dropping him down, I had to do it 10 times.
"(I did it) 10 times from five different angles. So, six-and-half or seven hours. Either, I was picking him and throwing (him) or else, he was picking me up and throwing me... So it was like the most difficult thing."
"When I used to walk out of the ring, I used to feel actually like a raped woman walking out... I don't think you... It was most difficult... I couldn't take steps. I would eat and then head right back to weight training. That couldn't stop."
The comment sent social media users into a tizzy, with many slamming the actor for his "callous remark" after a website carried the detailed quotes of Salman Khan as an 'interview' on Monday.
The National Commission for Women has taken note of Salman's comment and asked him to apologise for it within a week.