According to a special report from the European Court of Auditors (ECA), the Commission dealt in a satisfactory way with deficiencies identified in the Member States' management and control systems, but was less successful in obtaining assurance that its actions led to improvements in Member States’ management and control systems. In addition, the ECA also published a report which concludes that Structural and Cohesion Fund investments in transport infrastructure in seaports effective in only 11 out of the 27 projects.

The European Commission takes appropriate corrective actions when deficiencies in Member States' systems are identified, but the process to implementation is lengthy, according to the ECA's special report (Nº 3/2012). In this report, the ECA concludes that the Commission had some success in ensuring that financial corrections were correctly applied, but was less successful in obtaining assurance that its actions led to improvements in Member States’ management and control systems. In October 2011, Court of Auditors also considered that, although positive, results of ERDF funding to e-government can be improved.

For this reason, the European Court of Auditors (ECA) makes a number of recommendations to the Commission such as reducing the duration of the administrative procedure from identification of deficiencies until implementation of corrective actions; giving higher priority to its audit work on the audit authorities; disseminating checklists that serve as best practice to be followed by Member States authorities for their first level checks; and ensuring that financial corrections cover all expenditure incurred under deficient management and control systems.

On the other hand, the ECA also adopted the special report Nº 4/2012 which shows that only 11 of the 27 audited transport infrastructures in seaports’ projects co-financed by the Structural and Cohesion Funds in the 2000-06 programme period were effective. It therefore recommends to the Commission to strengthen the assessment procedure for Major Projects and Cohesion Fund Projects to improve the detection of serious weaknesses and the taking of appropriate action to remedy them and to make Cohesion Policy aid for the coming period conditional upon the existence of a comprehensive long term port development strategy (based on an assessment of needs) for all the ports of the relevant region.