The 27-year-old midfielder, who plays for Mumbai FC in the I-League, tested positive for banned drug tetrahydrocannabinol, the active chemical in cannabis, after a test conducted in January this year in the city of Pune.
"The National Anti-Doping Agency has banned Mehra for two years," the All India Football Federation (AIFF) said in a statement late Monday.
"Mehra tested positive on 4 February with AIFF imposing the provisional suspension on him from 10 February as per the guidelines of the FIFA."
Mehra is the second Indian footballer to be banned for doping after defender Arun Malhotra failed a test in 2002 and was stopped at the last minute from travelling with the national team for the Busan Asian Games.
NADA said Mehra had failed to explain how the drug got into his body, thereby inviting the harsher punishment rather than a suspension.
"Mehra was given an opportunity to explain but he had very little to offer by way of a convincing argument to prove how the substance got into his system," NADA said in a press release.
Despite having the world's second-biggest population at 1.2 billion people, India, where cricket is the main sport, remain a footballing minnow and are ranked a lowly 146 in the world.
The country did enjoy success in the 1950s and 1960s but have never played in the World Cup and their last Olympic appearance was in the 1956 Melbourne Games where they finished a commendable fourth.
The I-League, launched in 2007, is the country's top-tier professional league and enjoys support in the eastern state of West Bengal and southern states of Kerala and Goa.