Zafarul Islam Khan, a national Muslim newspaper editor, said on Monday the Archeological Survey of India (ASI) report is politically motivated.
He added it was written by people who want to see a Hindu temple built on the site of the former Babri mosque in Ayodhya.
He was speaking hours after a deadly bombing in Mumbai killed at least 50 people after the release of the report.
More than 2000 people died in clashes after the Babri mosque was destroyed in 1992 by Hindu zealots who said it was the birthplace of their god-king Ram.
Khan, editor of the Milli Gazette, said: “Muslims in India are stunned by this report and all Muslim groups have unequivocally condemned it.
"There were many preliminary reports on this issue which said there was nothing under the mosque, and then suddenly a temple appears out of the blue.
“The commission is headed by the same people that wanted the mosque demolished in the first place. They are clearly under the influence of the BJP Hindu right-wing government.”
He added: “It is very unfortunate because this is a very significant development but it has been rather overshadowed by today’s Mumbai blasts. This makes me suspect dark forces are at work.”
“Muslims in India are stunned by this report and all Muslim groups have unequivocally condemned it"
Zafarul Islam Khan
The report by the Archeological Survey of India was released on Monday by Lucknow High Court which will rule on how the dispute should be settled.
The report said there is evidence of a "massive structure" just below the Babri mosque after a five-month excavation of the disputed site.
"The lotus motifs, circular shrines, 50 pillar bases in association of a huge structure are indicative of remains which are distinctive features found associated with the temples of north India," the report said.
And a spokesman for the ASI rejected suggestions the report is politically biased.
“We are an indepedent body and are composed of Muslims as well as Hindus. We have only reported what we have found and any decision on the future of the site is up to the Indian courts and authorities.”
Muslims make up 12% of India's billion-plus population.
They claim the destruction of the mosque in 1992 signalled the end of security for Muslims in India.
They say the Babri mosque should now be rebuilt on the site.
But India's governing Hindu nationalist Bharatiya Janata Party reached national prominence by campaigning for a temple to be built in Ayodhya.
Prime Minister Atal Bihari Vajpaee said last week he would fulfill a promise to a recently deceased Hindu priest to build the temple.
In preliminary findings released in June, the ASI said it had found no evidence from a dig at the site that it ever held a Hindu temple.