If the Govt Agencies is having the GSTN , that means they further making Outward supply , hence you are liable to report such transaction under B2b in GSTR 1.
I am agree with venkaraddi sir... govt. agencies taken gst no. only for the purpose of deducting TDS... so u can't show in b2b..... further try to show the transaction In b2b by providing there gst no. ... I think there name will not auto populate in name column ...