Police said Dwijen Kalita, a panchayat secretary, and Mantu Ram Rabha, a middleman, were arrested based on an FIR filed by an official in Boko area.
Kalita is currently on deputation as panchayat secretary. The two are being interrogated.
While police did not mention the exact amount suspected to have been misaapropriated by them, it is likely to run into several lakhs.