The autobiography, which alleges that militant leader Jarnail Singh Bhindranwale was a creation of the Congress, had earned the ire of several Sikh radical groups.
In a statement here, Nayar said it had come to his notice that some parts of his autobiography had angered the Sikhs and several radical groups.
He had always raised his voice in favour of the Sikh Panth and had been a votary of Punjab, Punjabi and Punjabiat, the columnist said.
"I have a long history of activities and writings in this respect. I have no intention to hurt the sentiments of anybody," he said.
"As such, I have decided to delete the portions of my autobiography on which objections have been raised. These parts shall not be there in the next edition of the book.
"Even then, if I have hurt the sentiments of anybody, I feel sorry and apologise for the same," Nayar said.
The veteran journalist had stirred a hornet