The agency says these imports must be tested after samples of organic feed corn were found to have up to 20 times the permitted levels of aflatoxins.
"This is to prevent contamination of livestock feed in order to protect Canadian livestock and public health," the CFIA said in a release.
Aflatoxins are produced by a fungus and can cause serious health problems in animals such as cancer and birth defects.
The CFIA says aflatoxins can be transferred to milk and other animal products and could pose a threat to food safety.
Since May of last year, Canada has imported 34,735 metric tonnes of corn from India for use as livestock feed.
The CFIA says importers must sample the corn when it arrives in Canada and provide lab test results.
It says shipments of corn livestock feed from India will only be released when the test results show they are safe.
A group that represents the livestock and poultry feed industry said its members are aware of the CFIA notice.
Graham Cooper, executive director of the Animal Nutrition Association of Canada, said corn is blended in as an ingredient in livestock feed mainly for cattle, hogs and poultry.
Imports of corn from India make up a very small percentage of what is used by the feed industry, he said.
"The industry would immediately put its antenna up to make sure that it is guarding against contamination of its feed stocks," he said Monday.
The association, which represents 170 feed and ingredient manufacturers and distributors across the country, wasn't sure if the Indian feed corn was being imported by feed mills, brokers or directly by producers.
Cattle producers in western Canada tend to use barley rather than corn in feed.
The CFIA issued a bulletin to the industry in February that levels of aflatoxins found in samples of Indian feed corn exceeded Canadian regulatory standards.