Syed Ghayorul Hasan Rizvi said it was a "laughable" remark made to earn a few brownie points from the government.
"It is laughable and juvenile to connect madrassas with terrorism. One or two isolated incidents cannot be used to defame madrassas," he said.
"Nowadays, children who studied in madrassas are becoming IAS officers and earning fame in multiple spheres. Madrassas don't breed terrorists, they produce IAS officers," he added.
Waseem-ur-Rehman from the Deoband in UP cleared UPSC in 2008. He got 404th rank. Maulana Hammad Zafar from Madrassa Ali Arabia in Mau, Madhya Pradesh cleared the exam in 2013, he said.
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The Jamiat Ulama-I-Hind served a legal notice on Wasim Rizvi citing the 'defamatory' remarks. It sought for a written and unconditional apology from Rizvi and a payment of Rs 20 crore towards damages.
The minorities commission chairman said Rizvi's letter would have no bearing on the government's stance towards madrassas.
"His comment was meant to earn a few brownie points from the government. But I am confident that the government will pay no heed to his statements. It instead wants to modernize madrasas," he said.