"It is a political conspiracy at the behest of the BJP to tarnish my image," he said.
Prajapati said he did not know the woman who had levelled charges against him.
"However, I will honour the judgement of the apex court," said Prajapati, who has been re-nominated by the ruling party as a candidate in Amethi, which goes to polls in the fifth phase on February 27.
The apex court, earlier in the day, directed the Uttar Pradesh Police to file a status report in the case within eight weeks.
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The woman, who is from Chitrakoot, alleged she was raped by Prajapati and others for two years on the pretext of getting a plum position within the Samajwadi Party. She has also alleged her daughter was sexually harassed too.
At a rally in Siddharth Nagar, BJP president Amit Shah took a jibe at the Samajwadi Party for painting a "false picture" regarding its clean image, and alleged that the state occupied the top spot in murders and crime against women.
UP BJP chief Kesav Prasad Maurya alleged that Akhilesh shielded criminals and rapists and because of this the apex court had to intervene.
Prajapati is a close associate of SP patron Mulayam Singh Yadav and his tenure as the mining minister was under cloud, prompting the Allahabad High Court to order a CBI probe into the allegations of wrong doings against him.
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