Patel, political secretary to Congress president Sonia Gandhi, is in the eye of a political storm after the arrest of the two suspected Islamic State operatives from Surat.
One of them was Kasim Stimberwala who worked at Sardar Patel Hospital in Bharuch district where Patel had been a trustee.
In a letter to Home Minister Rajnath Singh, he said the BJP was trying to malign his image by dragging his name in the case.
"Those guilty, irrespective of faith or any affiliation, must be brought to justice. Your government has my unstinted support in this matter," he wrote.
Patel said matters of national security cannot be a "prisoner of politics" and should not be reduced to "baselessly maligning political opponents for petty electoral gains".
"This would be the greatest injustice we would be doing in our fight against terrorism... Therefore, I find it extremely disturbing that the ruling party in Gujarat is vitiating a serious ongoing investigation just ahead of the elections by making wild and unsubstantiated allegations," the letter read.
"Framing terror charges must be done by law enforcement agencies and the judiciary, and not by political leaders in press conference from party headquarters," the Congress leader said.
Gujarat Chief Minister Vijay Rupani had on Friday demanded Patel's resignation and had asked him to explain the circumstances behind the hiring of Kasim.
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