"Everything will become clear once the four-day questioning of the suspects is over," Salih Tuzcu, the police chief of the central city of Konya where 13 of the suspects were detained, told the Anatolia news agency.
He described the arrests as an "operation against a terrorist organisation".
Eighty-six people have previously been charged with involvement in a plot against the government of Tayyip Erdogan, the prime minister, which hard-line secularists accuse of promoting an Islamic agenda for Turkey.
A journalist and senior officials from a small nationalist party whose leader is already in custody were among those detained on Wednesday.
Officials said the detentions were ordered by the prosecutors handling the Ergenekon case on suspicion of seeking to overthrow the government.
Three unlicensed guns, various documents and computers were reportedly seized during the raids.
In the last 50 years, military coups have unseated four elected governments in Turkey, a predominantly Muslim but politically secular country seeking to join the European Union.
Some opponents of the government have said that the investigation is revenge for legal bid to outlaw the ruling AK Party and ban Erdogan and Abdullah Gul, the president, from party politics for allegedly undermining the secular system.
Istanbul's chief prosecutor filed the indictment last week on the Ergenekon case, which includes charges of forming an armed terrorist group and attempting to overthrow the government by force.
An Istanbul court must decide by July 28 whether to accept the case.
The 86 defendants named in the indictment include the head of a small nationalist party, journalists, and retired army officers.
Earlier this month, two senior retired generals, leading businessmen and journalists, all critical of the AK Party, were arrested and another indictment is being prepared for them.
The case has added to political concerns in Turkey generated by the case to close the AK Party for seeking to introduce Islamic rule.
Constitutional court judges will begin deliberating that case also on July 28.