The 10-point report raises doubts as to whether Croatia will be able to end negotiations by June as initially hoped.
The document "identifies areas where further substantive efforts are still needed" and stresses that "convincing and credible track records" are required.
Enlargement Commissioner Štefan Füle said he was "hopeful that this report will help the Croatian government and Croatian society as a whole to redouble their efforts in this crucial area".
The report, which is not legally binding, was drafted by the Commission based on information from the Croatian authorities, international organisations, NGOs and officials from EU member states.
The document outlines steps that must be taken in areas such as the independence and professionalism of the judiciary, the treatment of war crimes cases, corruption, the return of refugees and the employment of minorities. It states in particular that "most high-level corruption and public procurement cases have not yet reached the stage of court rulings".
A spokesperson at the Croatian Mission to the EU said they were "fairly satisfied with the assessment of the Commission" and the report was "useful to us in the final stretch".
Slovenian MEP Tanja Fajon (Socialists & Democrats), vice-chair of the European Parliament's delegation to the EU-Croatia Joint Parliamentary Committee, was more sceptical of Croatia's negotiation prospects following the report's publication. She said that "it is still possible to conclude the negotiations in June," but that this objective was "very ambitious". She added that "this depends on Zagreb, the ball is in their court".
Croatia's anti-corruption efforts have featured several high-profile cases in recent months, including the convictions of former Defence Minister Berislav Rončević and former Deputy Prime Minister Damir Polančec. Former prime minister and onetime champion of European accession Ivo Sanader is currently in jail in Austria on corruption charges and is awaiting extradition to Croatia.
