​To facilitate the handling and the implementation and monitoring of recommendations, each report/note contains a table specifying those recommendations that require a decision by the governing bodies and those that can be acted upon by the executive head.
 
The procedure for handling and processing reports/notes is described in articles 11 and 12 of the JIU Statute. JIU entered into specific follow-up agreements with a number of participating organizations secretariats. As of 2012, 14 follow-up agreements were in place. The “model agreement” endorsed by the United Nations secretariat is applicable to its funds and programmes but some have entered into specific agreement to enhance collaboration. These agreements, based on the principle of shared responsibility, define the steps and conditions for effective follow-up on JIU recommendations by the Unit, the secretariats of participating organizations and Member States. In fact, the systematic monitoring and thorough follow-up of the status and implementation of recommendations issued by oversight bodies is one of the most important elements of effective oversight. Following the General Assembly’s repeated call for the strengthening of the Unit’s follow-up system on the implementation of its recommendations, in particular in its resolutions 62/246 and 64/262, JIU has developed a web-based system to monitor the status of recommendations and receive updates from individual organizations.
 
The follow-up system aims at tracking the acceptance, the implementation and impact of the recommendations contained in Joint Inspection Unit reports, notes and management/confidential letters.  As such it is a critical tool for the dialogue of the Unit with its participating organizations.