Sushma Swaraj warned that the global online retailer, which has made a significant push into India in recent years, would have to issue an "unconditional apology" for selling the items, which were pointed out to her on Twitter.
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Ms Swaraj was contacted about the doormats on Tuesday afternoon by "Atul Bhobe", a Twitter user with 60 followers, who sent a screenshot of several Indian flag doormats and urged her: "Amazon Canada must be censured".
The doormats, just some of a range of similar products bearing the flags of various countries, were selling for C$35.99.
Within hours the external affairs minister, who is known for her active Twitter account, responded: "Indian High Commission in Canada: This is unacceptable. Please take this up with Amazon at the highest level."