Kemal Kilicdaroglu, the deputy chairman of the secular CHP opposition, said "This is an operation against the intellectuals of this country."
Hayati Yazici, the country's deputy prime minister, said nobody was above the law in Turkey.
He said: "The judicial bodies are authorised to deal with those who commit crimes. Turkey is on the right track."
Among those detained was Tijen Mergen, an employee of a unit of media group Dogan Yayin, the owner of Hurriyet, Turkey's top-selling daily newspaper.
Dogan Yayin has been embroiled in a legal battle with the government since it was fined $500m this year for alleged tax violations.
The fine came after months of public mud-slinging between Dogan newspapers and the government, prompting some, including the US state department, to question the level of press freedom in the European Union candidate country.
Government critics see the investigation into Ergenekon as revenge for a failed 2008 lawsuit to ban the AK Party on the grounds of anti-secular activities.
|Turkey's prime minister denies the case against Ergenekon is politically motivated
Recep Tayyip Erdogan, Turkey's prime minister and leader of the AK Party, denies the case is politically motivated.
Monday's arrests included the detention of Mehmet Haberal, the head of Baskent University in Ankara, Turkey's capital, and three former college heads in the Black Sea city of Samsun, in the eastern city of Malatya and in Bursa, west of Istanbul.
Universities have been bastions of the secularist elite, alongside the judiciary and the military, who resent the rise to power of the AK Party which has its roots in political Islam.
Police also detained Mustafa Yurtkuran, the acting chairman of the ADD, an organisation which supports the secular ideas of Mustafa Ataturk, the founder of modern Turkey
The group organised mass street protests in 2007 against the AK Party government's attempt to lift a veto on the wearing of Muslim headscarves in universities.
Ergenekon came to light more than a year ago when explosives were discovered in a police raid on a house in Istanbul.
The military, which is widely respected in Turkey, has unseated four elected governments either in outright coups or by strong political pressure.
It has denied any links to Ergenekon.