Prajapati and two other convicts Ashok Tiwari and Ashish Shukla were present in the court when the judgment was pronounced.
Gayatri Prajapati has been on the run since February 27.
Mulayam alleged that Prajapati was being treated like a "terrorist" and said he would take up the matter with the prime minister.
The case pertains to the issuance of mining leases in alleged violation of e-tendering process. The Allahabad High Court had ordered the probe.
"A non-bailable warrant has been issued against Prajapati after an FIR was registered against him in rape case. Serious question of constitutional morality and dignity arise on his remaining in the cabinet", governor said in a letter to CM seeking his "justification on retaining the minister".
The Congress on Monday nominated Bharatiya Janata Party turncoat Ashish Shukla against the saffron party's nominee, Sanjay Sinh, from the high-profile Amethi assembly seat in the upcoming Uttar Pradesh assembly polls.
The passport of rape accused Uttar Pradesh minister Gayatri Prajapati was impounded on Saturday and a look-out notice was issued against him, hours after Prime Minister Narendra Modi accused the Samajwadi Party and the Congress of chanting "Gayatri Prajapati Mantra".
The action comes close on the heels of Samajwadi Party supremo Mulayam Singh Yadav sounding a warning to party leaders, saying that action needed to be taken against those involved in land grabbing and other corrupt activities if the party wanted to return to power in the 2017 assembly elections.
Besides Yadav, the CBI is likely to question Gayatri Prajapati, who was arrested in 2017 following a complaint of rape by a woman residing in Chitrakoot.
He further contended that in his bail application, Prajapati stated that he had no criminal case pending against him but six cases were pending against him.
Notwithstanding a pre-poll alliance between Congress and Samajwadi Party, former state minister Ameeta Sinh on Thursday filed her nomination as a Congress candidate from Amethi seat which has been given to the ruling party for the high-stake Uttar Pradesh assembly polls.
Mulayam announced that sacked minister Gayatri Prajapati will be taken back in the UP cabinet.
Lucknow's Hazratganj police station on Saturday refused to register an FIR by IPS officer Amitabh Thakur, who was allegedly threatened by Samajwadi Party supremo and former chief minister Mulayam Singh Yadav.
SP has already fielded its sitting MLA from Gauriganj seat.
A departmental inquiry has also been ordered against the judge.
Despite both parties joining hands to fight the elections, they have fielded different candidates for the polls in this region.
The CM said his government has not deviated from its zero-tolerance policy on crime.
'Akhilesh's plan is simple.' 'He wants to lead the party on the strength of the infrastructural development his government has done, capitalise on the massive sympathy wave of young people in the state who dream of doing what he has managed to do -- defy a feudal, greying orthodoxy that occupies and sits on posts and positions never to leave.'
Apparently hinting at Amar Singh, UP CM says 'we will not let outsiders drive a wedge between us'.
Uttar Pradesh minister Gayatri Prajapati, who is evading arrest, on Monday failed to get relief from the Supreme Court which expressed unhappiness that its order on lodging of FIR against the SP leader was being given "political colour".
The announcements were made as per the compromise formula worked out by SP chief Mulayam Singh Yadav who asserted that "There can be no division in the party."
The IPS officer is currently posted as inspector general (civil defence).
The feud in Uttar Pradesh's first family has ended, with Chief Minister Akhilesh Yadav on Saturday night restoring all but one portfolios of Shivpal Yadav and promising to support him as SP's state unit president, a post from which he was himself removed three days back triggering the power tussle with his uncle.
The Congress vice president has eyes on the larger objective of his partnership with Akhilesh, which may provide the template against the BJP in 2019 Lok Sabha elections.
Blaming Akhilesh Yadav for "sleeping over" the demand for justice by a "beti" in the rape case against Gayatri Prajapati, Prime Minister Narendra Modi on Saturday said the voters in Uttar Pradesh have got an opportunity to perform the pind daan (last rites) of their "tormentors".
Senior IPS officer Amitabh Thakur, who has accused Samajwadi Party chief Mulayam Sigh Yadav of threatening him with dire consequences, is suddenly at the receiving end, with the Lucknow police registering a case of "rape" against him.
"There is no matbhed (difference) or manbhed (ill feelings) among our leaders," Yadav said.
A day after high drama at a key meeting of the ruling Samajwadi Party, its state unit chief Shivpal Yadav on Tuesday said all was well in the party as he visited Mulayam Singh Yadav's residence and was joined in later by Chief Minister Akhilesh Yadav.
Chandrapal, when approached by mediapersons, said, "False allegations have been levelled against me. I went to Police Lines to voluntarily deposit my service pistol. I was arrested there. I was told my name is there in the FIR." He clarified that he was not absconding or hiding along with the minister. "I did not even have any telephonic conversation with him (Prajapati)," he said.
Addressing an election rally, BJP chief Amit Shah said, "As soon as the BJP forms the government in UP on March 11, we would search (Gayatri Prasad) Prajapati even from the hell and send him to jail."
Claiming that the SP supremo had threatened him with dire consequences, Amitabh Thakur sought protection from the Centre.
Akhilesh was referring to the advertisement in which Bachchan is seen inviting tourists to visit the Wild Ass Sanctuary located in Little Rann of Kutch in the state.
Responding to the donkey remarks made by Akhilesh, Modi said the criticism of donkeys by the UP CM only reflected his 'casteist mentality' and 'the feeling of hatred does not suit him'.
According to an insider, "Winning is all that matters to the BJP. The leaders were warned that he was an undesirable character but they said look at his victory margin."
Controversy shrouds the expansion of the Akhilesh Yadav ministry on Monday with a social activist throwing a spanner by challenging before Governor Ram Naik the possible re-entry of tainted former Mines Minister Gayatri Prajapati.
Senior Indian Police Service officer Amitabh Thakur, who is locked in a tussle with ruling Samajwadi Party chief Mulayam Singh Yadav and took his fight to the Centre, was on Monday night suspended by the Uttar Pradesh government.
Since the Mahabharata the Yadavs have been known for infighting. And the 2017 UP election proved yet another example of that, says Nazarwala.
A number of royals have thrown their hat in the ring in the high-voltage Uttar Pradesh assembly elections.
As the Uttar Pradesh assembly election battle hits new lows, Rediff.com's Aslam Hunani walks you through all you need to know about the fifth phase of polling on February 27.
In an open rebellion that could split the ruling Samajwadi Party, Uttar Pradesh Chief Minister Akhilesh Yadav on Thursday night "declared" his own candidates for 235 seats against the official list announced by his father and SP supremo Mulayam Singh Yadav for the upcoming assembly polls.