"Amazon must tender unconditional apology," India's external affairs minister Sushma Swaraj said on Twitter. "They must withdraw all products insulting our national flag immediately."
"If this is not done forthwith, we will not grant Indian Visa to any Amazon official," she added. "We will also rescind the Visas issued earlier."
The doormat, sold by a third-party on Amazon's Canadian portal, was taken down late on Wednesday.
"The item is no longer available for sale on the site," a spokeswoman for Amazon said in an email.
Amazon's portal in Canada sells doormats fashioned around other national flags, but under Indian law any desecration of its flag is punishable with fines and imprisonment. Amazon's official support account on Twitter had earlier responded to angry user comments on Twitter by saying the mats were not being sold on their Indian portal and the concerns had been escalated.
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Swaraj tweeted that she had asked the Indian High Commission in Canada to take up the issue with Amazon, after it was brought to her attention by a Twitter user from India's financial capital of Mumbai.
Swaraj is a prolific user of the social media website and often responds to tweets directed at her.
Amazon is making a huge bet on India and has vowed to invest more than $5 billion as it takes on home-grown Flipkart and Snapdeal for a bigger share of the world's fastest growing internet services market.
In an event attended by Indian premier Narendra Modi in Washington last year, Amazon Chief Executive Jeff Bezos said India was the company's fastest growing region.
