The Internal Audit Cell was established in 2009. It works directly under the Vice Chancellor of the University. The University engages Internal Audit Officer and Internal Auditors from the drawn from the Organized Audit and Accounts Services of the Central Government. The Cell conducts audit of all the offices, sections, departments, colleges, centres, and directorates of the University from time to time. The Audit functions are broadly divided into two types – pre audit and post audit.

MANUU mobilizes its grants mainly from the generous grants allocated by the University Grans Commission on various heads of expenditure mainly four components each of Non-Recurring (Capital Assets) and Recurring (Operation & Maintenance) Grants. However, each component has sub-components covers specific requirements viz. Infrastructure, Equipment, Books &Journals, Furniture & Fixtures under Non Recurring component.