Ankara is pursuing a systematic campaign of intimidation against the Turkish media, including the prosecution and jailing of writers, and demands for those who challenge government policies or actions to be sacked, two independent investigations have concluded.

Reports issued in recent days by the New York-based Committee to Protect Journalists (CPJ) and the European commission point to a pattern of harassment of individual writers and broadcasters and official pressure on media company owners.

Sixty-one journalists are in prison in Turkey as a “direct result” of their work or news-gathering activities, said the CPJ. “Approximately 30% of the imprisoned journalists were accused of participating in anti-government plots or being members of outlawed political groups. About 70% of those jailed were Kurdish journalists charged with aiding terrorism by covering the views and activities of the banned Kurdistan Workers’ party [PKK] and the Union of Communities in Kurdistan [KCK].”

It continued: “More than three-quarters of the imprisoned journalists have not been convicted of a crime but are being held [awaiting] resolution of their cases. Articles in the penal code give authorities wide berth to use journalists’ professional work to link them to banned political movements or alleged plots.

“Some of the most frequently used articles criminalise basic news-gathering activities, such as talking to security officials or obtaining documents. Up to 5,000 criminal cases were pending against journalists at the end of 2011, according to Turkish press freedom groups.”

The CPJ also said it had detected increased internet filtering of domestic news sources, including opposition and pro-Kurdish media.

The European commission’s findings, part of the annual “progress report” on Turkey’s EU membership application, also make disturbing reading.

“The increasing incidence of violations of freedom of expression raise serious concerns and freedom of the media continued to be further restricted in practice. The increasing tendency to imprison journalists, media workers and distributors fuelled these concerns.

“High-level government and state officials and the military repeatedly turn publicly against the press and launch court cases. On a number of occasions journalists have been fired [for] articles openly critical of the government.

“All of this, combined with a high concentration of the media in industrial conglomerates with interests going far beyond the free circulation of information and ideas, has a chilling effect and limits freedom of expression in practice, while making self-censorship a common phenomenon in the Turkish media.”

The report said many prosecutions targeted writers, academics and journalists writing and working on the Kurdish issue, but also scholars and researchers. More than 2,800 students are in detention, mostly on terrorism-related charges. Legislation covering such offences was “imprecise and contains definitions which are open to abuse”.

The government has not commented on the CPJ’s findings, but the commission’s progress report provoked sharp criticism, with the minister for EU affairs, Egemen Bagis, rejecting it as a “broken mirror”, adding that it did not accurately reflect the situation in Turkey.

Burhan Kuzu, head of the parliamentary commission charged with writing a new constitution and a member of the ruling Justice and Development party (AKP), told CNN Turk television the report was rubbish.

“This is a report to be thrown in the trash. There is no trash can here, so I’m throwing it on the floor.” Kuzu then threw the report on the floor, saying: “Here, I’m throwing it into the trash.”

Kadri Gürsel, a leading newspaper columnist and chairman of the Turkish national committee of the Vienna-based International Press Institute said the media in Turkey was under constant pressure to toe the official line.

“More than half the print media are directly or indirectly controlled by the government’s cronies and its proxy capitalists. The other half is in a hostage situation,” Gürsel said. Owners and employees of opposition media faced the ever-present threat of being prosecuted or arrested, which led them to curb what they said or wrote.

“This stops them practising independent journalism. To be honest, news is not the main instinct, it is self-censorship. When news comes to the news desk, the first question that occurs, unavoidably, is: ‘Does this matter harm the government interest?'”

Although the prime minister, Recep Tayyip Erdogan, had accumulated “unprecedented power” during nearly 10 year in office, there was virtually no public scrutiny of the AKP and no investigations into the lifestyles and business interests of ministers and their relatives.

“Since 2008 [after the party began its second term in office], there has been not one single corruption case reported by the media that could or would hurt government interests,” Gürsel said.

A former national newspaper editor who asked not be identified said Erdogan had made a habit of singling out journalists whose pieces offended him, and demanding their sacking. But government pressure on media companies was usually more subtle, he said.

“You can never prove it, but I’m sure messages are sent [to media owners]. The government very often intervenes. And the media magnates want to secure sympathy or curry favours from the government. But they never leave their fingerprints,” the former editor said.

Far from feeling ashamed, Erdogan and his supporters appear to believe their actions are fully justified. A report this week in the Aksam newspaper quoted Ali Özkaya, a lawyer acting for Erdogan, as saying lawsuits opened on his behalf against people who have “insulted” him in the press have had a salutary effect.

“We have to underline that cases we’ve opened against press have been quite a deterrent; the wording of columnists has noticeably changed especially since 2003 [when Erdogan took office]. Reporters and columnists do not exceed the dose when making criticisms any more. Insulting comments or columns have been reduced to minimum.”