State Congress spokesman Mukesh Nayak said Chouhan's act was aimed at attracting Muslim votes in Madhya Pradesh, where Assembly election is due by the year-end.
Chouhan's gesture on Friday triggered a controversy and he faced criticism both within his party BJP and outside.
This was not the first time Chouhan had sported a skull cap but the controversy arose due to comments made by film actor Raza Murad, who was present at the Bhopal Eidgah where the Chief Minister was seen wearing the cap.
While the Bollywood actor did not name anyone, his barbs were apparently directed at Gujarat Chief Minister Narendra Modi, who has in the past refused to don skull cap.
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Murad's remarks triggered a war of words between him and BJP leader Uma Bharti, who did not appreciate Chouhan's Eid gesture, terming it as "cheap".
A state BJP spokesman, reacting to Murad's comments, said yesterday that if wearing a skull cap does not defile one's religion then what objections do members of a community have to the singing of "Vande Mataram".
In 2011, the Gujarat CM had refused to put on a skull cap offered by a Muslim cleric during his 'sadbhavana' fast.
While Modi had refused to wear the cap in order to appease his Hindu votebank, Chouhan's move was aimed at attracting Muslim votes, Nayak said yesterday.
Chouhan himself had tried to put a "cap" on the controversy, saying an occasion like Eid should not be politicised.