M. A. Ganapathy was initially allotted Uttar Pradesh Cadre and served there between 1987 and 1999. During this period, inter-alia, he worked as Senior/Superintendent of Police in districts like Kanpur City, Meerut, Allahabad, Nainital, Hardoi, Sonebhadra etc. The policing challenges in these assignments were varied and included tackling communal issues, city policing, serious crimes investigation, anti-dacoity operations, naxal problem etc.
