"We clearly have a situation that needs to be solved so that Turkey moves forward," secretary general Thorbjorn Jagland told a group of foreign journalists in Ankara during a visit.
Jagland said Turkey had some 16,000 cases pending in the Strasbourg-based European Court of Human Rights, of which about 1,000 concerned media freedom, a situation he said had "a chilling effect" on freedom of expression.
"Turkish courts and prosecutors need to have a better understanding of European standards of what journalists are allowed to write and say without being put in jail," said Jagland, who met members of Prime Minister Recep Tayyip Erdoğan's government to discuss media freedom.
Since coming to power in 2002, Erdoğan's party has earned praise for political reforms aimed at bringing Turkey closer to European Union norms and for liberalizing an economy that is now among the fastest-growing in the world.
But his government also faces accusations of trying to tame the media and smother opposition. Critics say the prime minister uses Turkey's harsh defamation laws to intimidate journalists and counter personal criticism.
According to the Organization for Security and Cooperation in Europe, there are 57 journalists in Turkish jails although Turkish media groups put the number at nearly 70.
Most are held under broad antiterrorism laws, for allegedly promoting terrorist propaganda, that allow for suspects to be detained for lengthy periods before being formally charged.
Turkey has fallen to 138th out of 178 countries reviewed for the World Press Freedom Index by Reporters without Borders, a media freedom pressure group, from 101st in 2007 due to the proliferation of lawsuits.
It is not uncommon for investigative reporters in Turkey to face prosecution. Journalists Nedim Şener and Ahmet Şık, known for articles they wrote about an alleged 2003 plot to topple Erdoğan's government, have been in jail since March.
The government rejects accusations that it curbs media freedom and says journalists are not in jail because of what they wrote, but for non-journalistic activities.
Gerard Stoudmann, special advisor to Jagland and media freedom rapporteur, said Turkey had "difficulty" understanding what is investigative journalism.
"Besides the issue of law, it's an issue of mindset, of how the judiciary and prosecutors see their roles," Stoudmann said.