ISTANBUL — Since the Turkish republic’s founding 87 years ago, the military has stood as unquestioned guardian of secular democracy, intervening when it deemed necessary to keep religion out of politics in this overwhelmingly Muslim nation.

But now, battered by allegations of corruption and scandal, the authority of the once-unchallenged military is being whittled away by an increasingly assertive and confident public. The critics are a diverse array of democracy advocates, head-scarf-wearing Muslim women, journalists and others who complain that the military’s grip on power has largely benefited wealthy and secular elites.

Old taboos are collapsing amid the new questioning of a military-political order established by revered national founder Mustafa Kemal Ataturk. Ceren Kenar, 25, a graduate student in Istanbul, recalled marching in the streets of Ankara to protest against a blunt military foray into domestic politics in 2007. She said that when she wasn’t detained, “that was the moment I knew Turkey had changed.”

Turks now freely discuss and criticize the military. Most remarkably, senior officers, once immune from any kind of prosecution, have been arrested in an alleged conspiracy to oust Prime Minister Recep Tayyip Erdogan’s party from power.

A secret organization

The officers are accused of taking part in an underground organization, known as Ergenekon, that allegedly plotted to overthrow Erdogan after he was elected in 2002. The arrests have deeply demoralized and rattled the military upon which Washington depends.

The United States wants Turkey to continue with democratic reforms, but it also wants its military to remain a strong, reliable ally in the region. President Obama signaled the importance of Turkey — which borders Iran, Iraq and Syria — a year ago when he made it his first international destination as president.

After visiting Ataturk’s tomb, Obama told the Turkish parliament that the founder’s “greatest legacy is Turkey’s strong and secular democracy.” That legacy is at the heart of Turkey’s current power struggle.

Erdogan is pushing a major overhaul that would amend the country’s 28-year-old military constitution with reforms including changes to statutes covering the prosecution of military officers. In a recent poll, 58 percent of respondents said Turkey needs a civilian constitution compared with 20 percent who said it doesn’t. Three months ago, a law was passed limiting the military’s role to guard against external threats rather than perceived domestic ones.

The Turkish military is not clearly controlled by civilian leaders — unlike that of the United States, where the president is commander in chief of the armed forces.

“The Turkish army chief of staff doesn’t consider himself subordinate to the minister of defense. He does not consider himself subordinate to the prime minister, either,” said Yasemin Congar, 43 and editor of Taraf, the two-year-old Turkish newspaper that has broken most of the Ergenekon stories.

“In Turkey, the elected governments have never been the real power,” she said. “That’s what’s changing now. It’s kind of an unwritten law that they always abide by the military. It’s the founder of the republic, guardian of the regime, guardian of secularism. Now it’s changing a bit. But it’s a very, very hard process.”

Because of her dangerous central role publicizing the Ergenekon plot, Conger travels with bodyguards. She is careful not to take the ferry to work across the Bosporus, the beautiful strait that splits Istanbul and separates Europe from Asia, presumably for fear that she could be assassinated and dumped overboard.

Ergenekon is maddeningly complex and filled with pulp-fiction plots such as alleged plans by the military to blow up mosques to create chaos. Some Turks say the stories sound too fantastical to be real. But many others say that they ring true in a nation where the military has a history of orchestrating coups to oust governments it doesn’t like.

For many, the most startling aspect of Ergenekon is that it is discussed at all, and that the military has not been able to quash it.

“The significant thing about Ergenekon isn’t that it’s happening — because there’s some amount of truth behind some of these allegations,” said a Western diplomat in Ankara who spoke on the condition of anonymity. “The significant thing about this is that they’ve managed to resolve these things up until now without any kind of crisis.”

Beyond more open criticism of the military, society is shifting in more subtle ways.

Symbolic change

Ataturk’s image is still just about everywhere, but when Turkey issued a new currency last year, the founder of the republic was put on only one side of the bill rather than both. The military no longer guards the parliament building, a symbolic change.

Still, the military has many fans who believe it has nobly guarded against religion undermining the nation’s secular character. Many here suspect, for example, that Erdogan wants to turn Turkey into an Islamic state.

Critics cite Erdogan’s push to allow women to wear head scarves at state universities — a major political issue here — and to make adultery illegal. He failed at both. His advocacy of taxes on tobacco and alcohol, both prohibited under Islam, also raised red flags.

Erdogan’s biggest political problem may be that he has failed to convince much of the traditional elite that he won’t take away their secular freedoms. One prominent critic, retired Brig. Gen. Haldun Solmazturk, said he doesn’t trust Erdogan to make decisions that will preserve Turkey’s secularism.

Still, many Turks are questioning whether Ataturk’s vision is appropriate in modern, diverse Turkey, a burgeoning economic and regional power with aspirations to join the European Union.

Kenar, the Ankara graduate student, predicted that protests against the military’s dominant role in society would continue to grow.

“The overuse of Ataturk created a generation like mine,” she said.