The European Commission provided for CPMA Extended Decentralised Implementation System (EDIS) accreditation on 30 of July 2004. Having EDIS mandate the CPMA is involved in implementation of other EU financing instruments (Structural funds) and special programmes (Schengen Facility, Kaliningrad transit, Ignalina Programme etc.).

The CPMA has been certified with the ISO 9001:2015 (LST EN ISO 9001:2015) standard, which is based on a number of quality management principles including a strong client focus, the motivation and implication of top management, the process approach and continual improvement. The Agency also holds the ISO 14001:2015 (LST EN ISO 14001:2015) certification for setting up an effective environmental management system and operating with full environmental responsibility.

In 2015, the CPMA integrated the acclaimed Lean management system to increase operational performance in accordance with strategic objectives of the organization.

After assessing the activities of the Central Project Management Agency, the European Commission has concluded that the Agency fulfils all of the necessary requirements for the additional Pillar-Grants. The new pillar now allows the Agency to directly manage EU grants. The Pillar Assessment is based on 7 criteria. Until now the CPMA, working with the Ignalina programme, had to comply with 4 out of the 7 pillars, positively assessed in 2010 and reassessed in 2017. In order to carry out new activities- to increase implementation of EU development cooperation programmes - CPMA had to get positive assessment from the European Commission of 5 pillars.