Sixty-eight-year-old Patel, a seven-time MP from Gujarat and political advisor of Congress president Sonia Gandhi, is fighting for a Rajya Sabha berth from the state where four candidates are in fray for three seats.
The BJP has named its national president Amit Shah, Union minister Smriti Irani and Balwantsinh Rajput for the polls which are scheduled on August 8.
The apex court said that the party had not challenged it earlier because the notification suited it.
A bench, headed by Justice Dipak Misra, however, agreed to examine the constitutional validity of the NOTA provision in Rajya Sabha polls, saying that the issue needed to be debated.
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"The Election Commission of India (ECI) had enabled the NOTA provision in 2014, which came into effect in 2015. You (Congress) did not challenge the provision when it suited you," the bench, also comprising Justices Amitava Roy and A M Khanwilkar, said and issued notice to the poll panel.
"We are not going to stay the notification. Even after the elections and results are declared as per the schedule, the matter will be heard on the constitutional issue," it said.
It listed the matter for detailed arguments on September 18 and directed the ECI to file its reply within two weeks on the plea.
The bench said that since the Centre has nothing to do with the notification, it was deleted from the list of the respondents.
At the outset, senior advocate Kapil Sibal, representing the Gujarat Congress leader, sought a stay on the notification, saying that if the NOTA provision was allowed in the Rajya Sabha polls, it would encourage "horse-trading and corruption".
"It is for the first time there are four candidates for three Rajya Sabha seats in Gujarat. If NOTA is not disabled in the state, which is witnessing a close contest, it will be a recipe for corruption and the MLAs may exercise the option to make their votes invalid," Sibal said.
Sibal replied that he was not afraid but, if the notification was not stayed, then the MLAs might exercise the provision and take money from the other side.
The apex court said that the poll panel's notification was not a state-centric one.
On being denied the stay, Sibal said, "Then it will make our pleas infructuous."
The bench then said it meant that the Congress MLA was not "genuinely concerned" about the legal issue.
Another senior advocate Abhishek Manu Singhvi, appearing for the Gujarat leader, said that it was a peculiar case where both the Congress and the BJP were on the same page.
Desai told the bench that senior advocate and Congress leader Vivek Tankha, who was in the courtroom, should assist it on the issue whether there was a NOTA provision when he contested the Rajya Sabha polls from Madhya Pradesh.
"How would I know? I was a candidate then, I was not a voter," Tankha, also representing the Gujarat leader, said.
Sibal intervened and said that it was an indirect election with proportionate representation and there was no scope for the NOTA provision as it was meant for direct elections.
The court said that the ECI's notification was not state- oriented and whether was it right or wrong needed to be debated as to whether NOTA will apply in the Upper House polls.
"The notification of the ECI is for Gujarat, West Bengal and Madhya Pradesh. The election should be taken in the widest sense. It has been already notified. Any interference will totally disrupt the polls," the bench said.
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