Government Contractor - Department GST to Show in GSTR -1 or Not

I am doing Government Contract Works and filing GSTR - 3B & GSTR - 1 regularly i want to know whether filing in GSTR - 1 i want to show the Government Department GST Number ( regular taken using PAN -  Not Tax Deductor  GST Taken using TAN ) or Not . I have filed GSTR - 1 using their GST regular number received at the time of Payment. now the department is telling  me u should not file in B2B dont use our GST and ask me to file the Turnover in B2C is that correct kindly help and do the needfull.