The prison chaplain organizes and coordinates Christian ministry in prison, ensuring that there would be conditions necessary for Christian ministry for all inmates. In addition to conducting worship services it is also the responsibility of the chaplain to be a counselor for all prisoners and prison staff.

The main work of the chaplains of the De fence Forces is to conduct religious services for conscripts, participate at the ceremonies of the military units and conduct prayers, accompany units on training exercises, hold services by monuments and memorials, counsel, deliver lectures related to ethics and morals, sometimes to organize events, etc.

The chaplain ministry was started after the re-establishment of the Republic of Estonia on 20 August 1991. In 2007 the UMC in Estonia is represented by five prison chaplains and two chaplains of the Defence Forces: Olavi Ilumets, Senior Chaplain of the Tartu Prison; Maksim Jefimtšuk, Senior Chaplain of the Social Rehabilitation Centre (at the same time Assistant to Igor Miller, Adviser-Chief Chaplain of the Prisons Department of the Ministry of Justice); Lea Traagel, Chaplain of the Tallinn Prison; Andrei Spiridenko, Chaplain of the Viru Prison; Johannes Kakko, Chaplain of the Houses of Detention of the Lääne Police Prefecture; Captain Raivo Nikiforov, Senior Chaplain of the Tapa Training Centre and Second Lieutenant Jana Laaneser, Chaplain of the Ämari Airforce Base.

The prison chaplain has unlimited rights to visit all inmates, including those sentenced to life imprisonment. In this way the prison chaplain is a bridge between society and the inmates. The chaplain is involved in the re-socialization of the imprisoned persons in cooperation with different rehabilitation centres. Senior chaplain Olavi Ilumets is the chairman of the Executive Board of the non-profit organization Rehabilitation Cent­re Valge Eesti as well as a board member of the Social Rehabilitation Centre in Tallinnwhere volunteer support staff from different churches are trained.

Raivo Nikiforov, ordained elder of the UMC in Estonia and Chaplain of the Defence Forces has served in foreign missions as chaplain on several occassions, in Kosovo, Iraq and Afghanistan. Raivo Nikiforov’s efforts during the years have led to a chapel being built at the Tapa Training Centre of the Estonian Defence Forces. Jana Laaneser, Chaplain of the Defence Forces worked in the Tartu Single Rescue Brigade in 2004–2005 and since October 2005 she serves at the Ämari Airforce Base, working with professional military staff.

Johannes Kakko is Specialist-Chaplain of the Rummu Prison since 2 January 2007. His responsibility is ministering to the inmates, organizing rehabilitation and crime prevention. Additional tasks are communication with prison staff, Christian counseling and delivering of death notices together with a police officer or alone. Implementation of police chaplains in Estonia is, however, still in the process of formation.