The Managing Authority in cooperation with National Authority establishes a Joint Technical Secretariat. It is placed in Haskovo, Republic of Bulgaria. JTS has an antennae in Turkey. The JTS (including its antennae as part of the same body) consists of equal number Bulgarian and Turkish experts contracted by the MA.

JTS provides daily help to the Managing Authority and the Joint Monitoring Committee of  the Programme and assists where appropriate the Certifying Authority and Audit Authority in carrying out their respective duties. The JTS also takes part in preparation and implementation of the decisions of Joint Monitoring Committee and carries out usual duties of a secretariat.

The JTS is in particular responsible for the following joint tasks:

• participation in planning and organisation of programme information campaigns and other activities related to raising public awareness on the programme;
• establishing and managing a joint projects data base and project partners data base;
• supporting projects generation and development,
• supporting MA and National Authority for the preparation of all standardised forms for the implementation of Programme such as application package, evaluation, contracting, implementation, monitoring and reporting,
• preparing the full application package for CfPs and submit to MA and National Authority for approval,
• advising beneficiaries on the implementation of operations and financial administration;
• receiving and registering of applications submitted;
• performing a formal check of project applications in terms of administrative compliance and eligibility;
• presenting a work plan via the Managing Authority to the Joint Monitoring Committee once a year for approval;
• organising all meetings and events, draft the minutes, prepare, ensures the administrative management of tasks and services;
• providing secretariat services for Evaluation Committees and submitting the results of the project technical evaluation sessions to the JMC;
• monitoring of project implementation, collecting of information from the lead beneficiaries and updating data in the Management Information System;
• coordinating the work of the controllers and providing cross-check of the certified activities;
• collecting and checking project reports from the lead partners before submitting to the MA;
• assisting the MA in preparation of the reports on programme implementation;
• receiving requests from the lead beneficiaries on any modifications as well as preparation of addendums to projects and submitting them to MA or JMC respectively for approval;
• cooperation with the programme implementing authorities in Bulgaria and Turkey, and with other territorial cooperation programmes;
• collaboration with central, regional and local stakeholders involved in the CBC Programme.