The raids were ordered after some members of Hezbollah and the Kurdish seperatist PKK group, freed earlier this month after spending over a decade in prison without being sentenced, failed to report to police stations and went underground.
The Supreme Court on Friday ordered the rearrest of the dozen absconders, but they were not found and police suspect that some have fled to Iran or Lebanon.
The largest raids overnight took place in the southeastern cities of Gaziantep and Adana.
Dozens of members of Hezbollah, a Sunni Muslim movement not related to Lebanon's Shi'ite Hezbollah, were freed earlier this month along with a few members of the rival Kurdistan Workers Party (PKK).
Courts that ordered their conditional release had acted on a change to the criminal code that came into effect on January 1, and which put a 10-year cut-off for a prisoner to be held without being sentenced.
Many Turks voiced anger over televised scenes of jubilant Hezbollah supporters greeting their freed leaders and alarm spread over a potential threat to national security.
Some of those released had been convicted by local courts of involvement in killings during the 1990s, but had not had their sentences endorsed by the Supreme Court of Appeals -- a requirement under the Turkish system.
The PKK, a Kurdisht separatist movement, and the Islamist Hezbollah are fierce rivals in the southeast, where Hezbollah has strong support. According to some analysts the Turkish Hezbollah has become less militant and more mainstream over the years.
Turkish media has reported that some 50,000 prisoners have applied for a review of their cases following the change in the penal code.