The instruction, which came into effect from midnight on Tuesday, has been sent to all air and sea ports, besides the department of posts asking them to thoroughly check all freight arriving from Yemen and Somalia.
"Since India has witnessed many terror attacks in the past, we don't want to take any chance," a home ministry official said.
Several countries, including the United States, Canada and Germany have banned freight services from the Arabian peninsula country after two parcel bombs addressed to Jewish institutions in Chicago and containing the lethal explosive pentaerythritol tetranitrate hidden in ink toner cartridges were uncovered last Thursday on cargo planes en route to the US.
The government also does not want to take any chance, as US President Barack Obama will arrive in the country on November 6 on a three-day visit.