The Information and Communication Technologies Authority (BTK) has fined Twitter 150,000 lira (USD 50,700), the first time it has issued such a penalty to the company.
Despite repeated warnings, Twitter failed to withdraw content "praising terrorism, targeting the security forces and inciting hatred and violence", it said.
There were no further details on the nature of the offending content but Turkish officials have repeatedly expressed irritation over the presence of material on social media in favour of the outlawed Kurdistan Workers' Party (PKK).
The authorities have repeatedly imposed temporary blocks on Twitter and other social media during times of crisis.
President Recep Tayyip Erdogan has a chequered relationship with Twitter, previously comparing social media to a "knife in the hand of a murderer" and saying "I don't like to tweet, schmeet."
But in February he started tweeting for the first time from his personal account @RT_Erdogan, which has now become one of his main communication platforms.
Erdogan's suspicion of social media dates back to the mass protests in June 2013 against his rule, which were largely mobilised by posts on Twitter and Facebook.
That ban on social media was later overturned by the country's top constitutional court.
In April this year, Turkey also blocked access to Twitter, Facebook and YouTube over the publication of images of a Turkish prosecutor killed by leftist militants during a hostage standoff.