Fewer than 20 retired officers, including several generals were being held, as police were stopped from serving warrants on dozens more after the intervention of the chief prosecutor of Istanbul.
The latest detentions of high-ranking members of the once untouchable military will deepen mistrust between the government and a secular establishment led by the generals and senior judges.
Istanbul Chief Prosecutor Aykut Cengiz Engin told reporters he had replaced two junior prosecutors who had ordered Monday's burst of detentions across 14 provinces, but gave no details.
His action illustrated the struggle between the senior judiciary and more junior prosecutors said to have sympathies with the ruling AK or Justice and Development Party.
Accounts of how many officers were actually detained before Engin ordered a stop varied.
NTV news channel reported that six people were brought to court on Tuesday, including former National Security Council General Secretary Sukru Sariisik.
Both the Istanbul chief prosecutor's office and police declined to comment on the detentions, and the state-run Anatolian news agency gave no figure on the number being held.
Turkey, which has the second largest army in NATO, was first rocked by an investigation into the alleged "Sledgehammer" plot in February, when the first round of arrests were made.
Scores of officers were detained then and in another wave of arrests, but most have been freed on bail pending indictments.
However, 12 of those detained and then released were sent back to jail on Tuesday pending trial. They were among 21 suspects whose rearrest was ordered on Sunday by a Turkish court.
Among them is retired four-star general Cetin Dogan, the former head of Turkey's prestigious First Army. He is being treated for a hernia in hospital.
The military says there was no conspiracy and Operation Sledgehammer was merely a war game exercise presented at a seminar. The operation involved bombing mosques and provoking Greece into shooting down a Turkish warplane to create a war like situation and destabilize the government.
Turks have been stunned by the procession of senior officers, including the former heads of the navy, air force and First Army, pulled in by prosecutors.
Prime Minister Tayyip Erdogan is trying to push through constitutional reforms that critics say would allow the AK to pack the superior court benches with its own nominees.
The AK denies having an Islamist agenda, and says the reforms are needed to strengthen Turkey's democracy and meet norms needed to gain entry to the European Union.
The government mounted its campaign for constitutional changes after being angered by the senior judiciary's suspension of four prosecutors behind the detention of a colleague who had been investigating an Islamist group in eastern Turkey.
Parliament is expected to vote on the reform package later this month and, if the government fails to get the two-thirds majority needed, Erdogan intends to call a national referendum.
Previously untouchable, the military's influence has waned because of political reforms undertaken since Turkey launched its bid for EU membership in 2005.
Few analysts believe the military would launch a coup, though it has overthrown three governments since 1960, and pressured Turkey's first Islamist-led government into resignation in 1997.
A more likely risk to political stability could come from Turkey's Chief Prosecutor Abdurrahman Yalcinkaya. There is speculation that he could launch another bid to have the Constitutional Court order the dissolution of the AK.
The prosecutor narrowly failed to have Erdogan's party banned in 2008 on grounds that it hade become a focal point for Islamist activity.
Investors in Turkey are uneasy over political developments, but its stock market, riding a wave of optimism over global economic recovery, hit an all time high on Monday, while the lira currency has held steady.
