"If Ind give up on Hinduism, they will also be solving most of their problems. What with all the piss drinking and dung worshipping," she had tweeted on September 9.
The tweet invited backlash on social media as users slammed her for the tweet and drew parallel with messages of Pulwama terrorists who killed 40 CRPF jawans in February this year.
Khan later deleted the tweet, apparently in a bid to avoid being "misinterpreted".
"I have taken the tweet down so that I am not misrepresented," she said, before apologising for what she had said.
"I wholeheartedly apologise for my earlier tweet. It was ill considered and unacceptable. I deleted it. I didn't mean to disparage Hinduism or hurt anyone's feelings. It doesn't reflect my beliefs and principles. Please accept my sincere regret. I'll be off Twitter for a while," she said on Wednesday.
"You can read that tweet a 100 times. Nothing, Absolutely Nothing justifies it. I'm a Muslim but even I can't forgive you for what you said, I doubt Hindus would or even should," retorted one Twitter user.
NPR said that it regrets the unacceptable tweet by New Delhi-based producer Furkan Khan.
"This comment does not reflect the views of NPR journalists and is a violation of our ethical standards. She has publicly apologised for her tweet and has resigned from NPR," NPR said.
Messages expressing Hindu-hatred, often emanating from Pakistan, have exploded on social media following the abrogation of Article 370 of the Constitution which granted special status to the former state of Jammu and Kashmir.
( With inputs from IANS )