"Our order is only the registration of FIR, nothing else. Let the police investigate and report to us. We never ordered arrest. If an NBW (Non-Bailable Warrant) is issued you have your remedies," the court told the lawyer of Mr Prajapati, who was last seen in public around two weeks ago.
The 49-year-old minister is accused by a woman of raping her and also attacking her young daughter. The woman said she moved court only when her complaint was ignored by the police. An FIR was finally filed only when the court stepped in.
Mr Prajapati's lawyer argued that he was not given a chance to speak in court before the FIR was filed. He also said the court was never informed after the case was filed, so moves to arrest him should be stopped.
The court said, "When we passed our earlier order, the UP government lawyer was there. We repeatedly asked him. Now it is taking a political colour."
On Sunday, Uttar Pradesh Governor Ram Naik wrote to Chief Minister Akhilesh Yadav asking why Mr Prajapati was still a member of his cabinet despite the allegations against him.
The minister has become a massive embarrassment to Akhilesh Yadav and his government in the middle of elections in Uttar Pradesh.
The Chief Minister had sacked Mr Prajapati for corruption last year but was forced to take him back, reportedly at the instance of his father Mulayam Singh Yadav.
Throughout the campaign in Uttar Pradesh, Akhilesh Yadav confronted taunts by Prime Minister Narendra Modi and his BJP on the tainted minister.
On Friday, Akhilesh Yadav told NDTV, "What I can say is that because the Supreme Court has issued him a notice, the government will cooperate in every way possible. Even I want the truth to come out."
Urging Mr Prajapati to surrender, he added, "In a democracy, in some circumstances you are forced to give some people a ticket. I have tried my best to keep the party clean."