It’s the Indian Foreign Service (IFS) where the Muslims are the most under-represented at barely 1.6%. That is 10 of a total of 619 (IFS cadre strength according to Expenditure Reforms Committee 1999-2000 documents) officers.
The seniormost Muslim IFS officer is Talmiz Ahmed, who is presently Director General of Indian Council of World Affairs. His immediate junior is Additional Secretary Arif Khan at the South Block.