Tds directly deducted by govt like govt teacher

How does an organisation file a TDS return when tax is deducted by the government and a net remittance is received by the organisation from the government? Meaning if 100 was receivable from the government ( for say salary), the government deducts 10and remits 90to the organisation. The organisation in turn gives 90 to the teachers. The organisation gives a salary certificate to the teachers at the end fo the year. The TDS software we have has a provision for a book entry, but it also asks for a challan at the same time. How do you make a TDS return in such a case? Any help would be appreciated