The commission's report on Turkey's progress made no clear recommendation on whether to suspend accession talks with Turkey, which began 12 months ago.
The report said the commission would make "relevant recommendations" ahead of an EU summit in Brussels in mid-December to decide on the issue.
In a key criticism, the report said Turkey was continuing to deny access to its ports to ships flying the flag of the Republic of Cyprus, creating a barrier to free trade.
The report also pointed to the continuing political influence exercised by the Turkish armed forces, limitations on freedom of expression, the continuing use of torture and ill treatment of prisoners, and the use of excessive force by the country's security forces.
It also complained about a lack of protection of the rights of women and minorities, including the country's Kurdish population.