The alleged incident also drew criticism from the Centre's BJP-led government, which said religious discrimination cannot be allowed.
Management graduate Zeshan Ali Khan had applied for an opening in the company on May 19 and, according to him, he received a response within 15 minutes which said they hired only non-Muslim candidates.
"Thanks for your application. We regret to inform you that we hire only non-Muslim candidates," the company said in response to his application.
"I applied for a job day before yesterday in the evening at 5:45 PM and within 15 minutes I get a reply from them that we regret to inform you, we don't hire Muslims. We only hire non-Muslim candidates. I was quite shocked when I read about this, I took a screen shot of it and posted it on Facebook," he said.
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Even as his social media posts triggered an outrage against the company, it sent a regret mail to Khan, blaming a trainee in its HR team with no decision-making powers for the "blunder".
"It was a blunder and personal mess created by one of our trainees who has no decision making power. We have 61 employees in our office here including one Muslim in the HR team," Hari Krishna Exports Private Ltd said in the mail.
"If there is any truth in this, it is unfortunate. An inquiry should be conducted," he said.
Reacting to the controversy, Minister of state for Minority Affairs Mukhtar Abbas Naqvi said, "A person's caste, region or religion cannot be a demerit.
"Discrimination on the basis of religion is neither allowed by our system nor the Constitution. If there has been case in which he (Zeeshan) was denied or fired from the job only on the basis of his religion, then I feel its not right," Naqvi said.