Shahabuddin had offered the conditional support to Modi in a letter written on November 16.
Three powerful organisations - the Jamiat Ulama-e-Hind, Jamaat-e-Islami Hind and the Milli Council - said they disagreed with Shahabuddin and were not sounded out on the issue.
They also alleged that the organisation, under the aegis of which Shahabuddin wrote the letter to Modi, was now 'defunct'.
Niaz Farooqui, the secretary of Jamiat Ulama-e-Hind, the country's largest Muslim organisation, said: "The Jamiat was not consulted. In any case, we don't agree with its contents."
Disavowing the letter, Jamaat-e-Islami Hind political secretary Mohd Ahmed said the Jamaat's view was that Modi "should be tried for his role in the 2002 riots". Dr Manzoor Alam, the chief of Milli Council, another outfit in the umbrella organisation of which Shahabuddin is convenor, said these were Shahabuddin's "personal views".
Shahabuddin had stated in his letter that Muslim voters saw a shift in Modi's "attitude" now.