Sanjay Pandey, scientist at the Board which functions under the water resources ministry, and technician Chander Prakash Midha of the IMT, a body under the Council of Scientific and Industrial Research, are named in the FIR.
The FIR has said both connived to get money from industries in Haryana and Punjab.
The applications were allegedly forwarded through a regional CGWB officer along with recommendations for issuing the NOC to use ground water for industrial purposes, the FIR said.
CGWB is responsible for regulating the use of ground water and issuance of NOCs to various private and government institutions.