The indictment is seen as the latest episode in an ongoing power struggle between the government and secular groups supported by the military and other state institutions.
They include the judiciary and some trade groups, who accuse the government of attempting to raise Islam's profile in Turkey.
Turkey's military, which staged three coups in the past, has criticised the government for allegedly eroding the secular system.
But senior military officers are believed to have appeased some members within its ranks by occasionally issuing harsh statements against the government.
Without the backing of the military command, retired generals would have a very hard time staging a coup, and such attempts in the past have always failed, analysts say.
The military has returned power to civilians after restoring order following coups. But the alleged plots indicate the extent of uneasiness and animosity felt towards the current government.
If the plots are confirmed, they have come at a time when the government is spearheading efforts to strengthen democracy in Turkey in the hope of getting the country admitted to the European Union.
Opponents of Recep Tayyip Erdogan, the prime minister, say the charges are part of a government attempt to silence critics.
"This is a campaign to defame people who speak against the government,'' Onur Oymen, a member of the secular opposition party, the Republican Peoples' party, said.
Arms and explosives
Engin did not name those charged, but the suspects, including ex-army officers, lawyers, a small leftist and nationalist political party leader and an author critical of Erdogan, were detained after police uncovered a supply of hand grenades at the house of a retired non-commissioned officer in Istanbul last summer.
Forty-eight of the suspects have been jailed.
The investigation was deepened after Erdogan vowed to crack down on "deep state" gangs, a network of agents driven by hardline nationalism who may be taking the law into their own hands to target perceived enemies.
Three prosecutors have unveiled what they say is an intriguing net of ties between members of a secularist and nationalist group, called Ergenekon.
The prosecutor accused the group of being behind attacks on Turkey's administrative court and the pro-secular Cumhuriyet newspaper in 2006.
The attacks infuriated secularists and led to demonstrations against the government.
Engin said the current 2,455-page indictment also accuses suspects of possessing explosives and arms as well as obtaining classified documents and provoking military disobedience.
The prosecutor said an additional indictment is being prepared against a dozen other people, including two senior retired generals, who were arrested early this month for their alleged ties to the group.
The two would have been serving officers when the coup plots were being devised, newspapers have reported.
In another court case, Erdogan's government is facing possible closure by the constitutional court for alleged anti-secular activity.