After Encarnacion explained the mistake, Indian officials contacted the NYPD shooting range to verify his story, a source said.
He is out on bail but barred from leaving India until his case is resolved. His next court date reportedly is April 19.
Encarnacion, who joined the force in 2004 and works out of the 25th precinct in Harlem, was accused of violating India's Arms Act of 1959, officials said.
A source familiar with the case said charges are expected to be dismissed because, since he carried no gun, there is little evidence Encarnacion had any intention of using the ammo.
In the case involving Khobragade,, the Indian diplomat was arrested in Manhattan last year and accused of paying her nanny as little as $3 an hour.
In March, Manhattan Manhattan Federal Judge Shira Scheindlin tossed the indictment against her, saying Khobragade, who touted women's rights in her position at the Indian consulate in New York, had diplomatic immunity when the indictment was filed in January.
