Mukesh Kumar and Kapil Kumar Rae of Sitamadi district in Bihar was gunned down in Sarlahi district yesterday evening, they said.
Kumar and Rae were in the "criminal list" of Indian police, Nepali Police was quoted as saying by My Republica.
The bodies were recovered this morning, Senior Superintendent of Police Ramesh Kumar Khadka said.
Both have been shot from behind. The bodies will be handed over to Indian authorities after post-mortem at a hospital, the report said.