Sushma Swaraj tweeted that Amazon should issue an "unconditional apology" and withdraw the "insulting" products.
Failing this, she said India would rescind current visas for Amazon officials and not grant any more.
Amazon said it had removed the doormats from its site.
In a series of tweets, Ms Swaraj asked the Indian High Commission in Canada to take up the issue with Amazon after it was brought to her attention by another Twitter user.
"Amazon must tender unconditional apology. They must withdraw all products insulting our national flag immediately," she said.
"If this is not done forthwith, we will not grant Indian visa to any Amazon official. We will also rescind the Visas issued earlier.
The doormats, which were being sold by a third-party and described as "personalised durable machine-washable indoor/outdoor items", were removed from the site on Wednesday.
"The item is no longer available for sale on the site," an Amazon spokeswoman said in an email.
Amazon sells doormats featuring flags of other countries but in India desecration of the flag is punishable with fines and imprisonment.
Last June Amazon found itself in a similar controversy over sales of doormats illustrating Hindu gods.
The row comes as Flipkart, India's biggest online retailer, is involved in a fierce battle with Amazon over market share.(BBC)