The issue has snowballed into a controversy with the National Commission for Minorities saying it will conduct an inquiry if there is any truth in the matter.
Management graduate Zeshan Ali Khan applied for an opening in the company on May 19.
However, the company replied to him saying that they hire only non-Muslim candidates, according to Khan, who shared the details on his Facebook page.
"Thanks for your application. We regret to inform you that we hire only non-Muslim candidates," the company said in a 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.
Khan said he subsequently received a 'regret' mail from the company after his social media post generated sharp reactions.
The company said it was a "personal mess" created by a trainee in the HR team.
"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, area or religion cannot be a demerit.
"Discrimination on the basis of religion is neither allowed by our Constitution, nor by our administration. 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," he said.
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