Mumbai FC midfielder Nishant Mehra's 'A' sample returned a positive result following a test conducted in Pune, the AIFF said in a statement on its website.
"The midfielder will be appearing before the National Anti-Doping Agency (NADA) panel tomorrow [Thursday]," the statement said.
"Nishant's 'B' sample will also be tested in his presence before appropriate action is taken against the player."
In January, NADA started in-competition testing in the I-League, India's national football league, at the request of the AIFF.
Mehra tested positive for Tetrahydrocannabinol, which is found in cannabis and is on the World Anti-Doping Agency's in-competition banned list, a NADA official said.
"This is the first positive case we have got from the I-League. The report was sent to the footballer on February 7 [Monday]," the official told Reuters.
"For this substance, there is no need to provisionally suspend the player and so an immediate suspension has not been issued. A decision will be taken after the 'B' sample test."
Doping has been a recurring problem in India with weightlifting producing the highest number of offenders.
October's Commonwealth Games in Delhi was also hit by several failed drugs tests relating to banned stimulants.
