Security officials in Punjab said today that they had found the bodies of 41 men, women and children who were tortured to death by Sikh militants in the months that the militants held control of the Golden Temple in Amritsar. The Indian police and military stormed the temple complex in May and ousted the Sikh rebels.

The police said that the bodies were discovered during a three-month cleanup of debris at the temple, and that the toll was nearly twice the number that the police had reported finding two months ago. The bodies were reportedly buried under mounds of excavated soil during the year that the Sikhs held control of the complex.

''Several of the terrorists confessed to torturing and killing people who had opposed them or refused to give them money,'' said a senior security official in Amritsar. Other officials said the victims were people accused by the extremists of being police informants.

The discovery of the bodies and of what has been described as a torture chamber has caused widespread dismay among Sikhs and has led to new denunciations of the militants by mainstream Sikh leaders. The police said thick wooden and cloth paddles used to beat victims were found in a room facing the Golden Temple, Sikhdom's holiest shrine. Some Sikh leaders have dismissed the police reports as exaggerations and Government propaganda.