External Affairs Minister Sushma Swaraj warned on Twitter that she could deny Indian visas to Amazon employees if the company did not apologize and "withdraw all products insulting our national flag immediately."
"If this is not done forthwith, we will not grant an Indian visa to any Amazon official. We will also rescind the visas issued earlier," Swaraj tweeted.
The doormats were being sold by a third party and other mats showed other national flags, including the U.S., U.K. and Canada.
Swaraj ordered the embassy in Canada to take up the matter with Amazon "at the highest level."
The site removed the Indian-themed product, following Swaraj's Twitter threat.
The doormats had outraged many people among the Indian diaspora in Canada, who posted pictures of them on social media and urged the foreign minister to formally object.
In India, insulting the national flag is punishable with fines and imprisonment.
Last year, there were protests after the online marketplace offered doormats depicting Hindu gods.
(AP)