This paper aims at examining the institutional framework within which Special Units (SUs) in Cypriot secondary education operate. The establishment of SU targets to facilitate the education of pupils defined as having special educational needs (SEN) in mainstream schools, and their operation is governed by the 1999 law and subsequent amending acts and circulars. Neither the operation of the SUs and the institutional framework that guides their operation have yet been investigated. The main aim of our research was to investigate teachers' and parents' views of the way in which SUs function, as well as their opinions of the legislative sections relating to the special units. This process led to the creation of a critical approach called the Institutional Framework for Special Units in Cyprus. Lastly, the participants were asked to propose ways in which the SUs could operate an inclusive environment. This paper presents qualitative research conducted in three secondary schools in Cyprus. Our sample consisted of 52 participants (heads, special education associate administrators, assistant heads, teachers, parents) over a five month timespan (September 2017-February 2018). The results lead to the conclusion that immediate action for further improvement and change is imperative, primarily for the benefit of pupils defined as having SEN.