"There is no proof with the police against Prajapati," said Mr Yadav, a former Uttar Pradesh Chief Minister.
"A conspiracy is being hatched against him... He is innocent and is being meted treatment like terrorists," he added.
The seasoned leader also hit out at the BJP government and accused them of vendetta politics.
"The BJP government is following political vendetta. I will meet the Prime Minister and, if needed, the President to apprise them of the matter," he told reporters after the meeting.
A Protection of Children from Sexual Offences (POCSO) court will frame charges against Prajapati on July 3 and six others in the case, according to news agency PTI.
Mulayam Singh Yadav had visited the jail yesterday to meet Prajapati. However, he didn't get the required permission as it was an off, on occasion of Eid. Today, the Samajwadi Party patriarch spent over an hour with the former minister.
(with inputs from PTI)