In a separate development on Friday a further 18 soldiers were detained over the plot, in the second wave of arrests after 49 military officers were taken in on Tuesday.
The action over the alleged plot, known as Operation Sledgehammer, has seen Turkey's largest-ever crackdown on the military.
Recep Tayyip Erdogan, Turkey's prime minister, said on Friday that no one should consider themselves "above the law", in what was seen as a warning to the army.
"Those who make plans behind closed doors to crush the people's will must see that from now on they will face justice," he told a gathering of his Justice and Development Party (AKP).
"No one is above law, no one has impunity," he said.
Senior figures released
The latest developments come as Turkish prosecutors prepare to question Cetin Dogan, a retired four-star general accused of leading the purported 2003 plan to topple the government.
It follows a decision late on Thursday to release the three most senior figures questioned so far - Ozden Ornek, an ex-navy chief, Ibrahim Furtina, a former air force commander and Ergin Saygun, the former number two of the general staff.
A prosecutor handling the probe said Ozden and Firtina were released because there was no risk they would flee. Saygun was ordered to regularly report to police.
The trio walked free following crisis talks in Ankara between Erdogan, Abdullah Gul, Turkey's president and Ilker Basbug, Turkey's army chief.
The leaders sought to ease tensions between the government and the military over the investigation, saying that the "problems will be resolved within the constitutional order".
"The public must be assured that matters will be handled in line with the law and everyone should act responsibly not to damage institutions," Recep Tayyip Erdogan, the Turkish prime minister, Abdullah Gul, the president and General Ilker Basbug said in a joint statement.
Anita McNaught, Al Jazeera's correspondent in Istanbul, said despite the talks questions still remain over whether the army will co-operate with the investigation.
"What everyone has been saying from the moment this started is 'what will the army put up with?
"The army is known for being able to draw a stern line in Turkey when it feels it needs to. There are a number of areas in which the Turkish army might object, might object to the jurisdiction of the Turkish courts for example."
"Only recently serving members of the military did not get tried in civilian courts - now that process is evolving," she said.
Operation Sledgehammer is said to have been drawn up and discussed in 2003 within the Istanbul-based First Army, shortly after the Justice and Development (AK) party came to power.
It was not known whether the suspects made any move to activate the plan, first reported in January by the Taraf newspaper.
The arrests have fuelled political strains and unsettled financial markets in the country, adding to tensions generated by a clash between the ruling AK Party and the secularist army and judiciary.
The suspects have reportedly denied the allegations, which include plotting to blow up mosques and kill some non-Muslim figures to foment chaos and trigger a military takeover.
Other senior military officers have been indicted on charges of planning a separate plot by a far-right group known as "Ergenekon" to overthrow the government.
|The army has regarded itself as the guardian of a secular Turkish state [Reuters]
That trial is ongoing. Critics of the government say the Ergenekon case has been used to target political opponents.
The AK party, with its roots in political Islam, is accused by some nationalists of having secret plans to turn Turkey into an Islamic state.
The government rejects those claims, saying its intention is to modernise Turkey and move it closer to EU membership.
In 2008, the AK party narrowly escaped being banned for violating Turkey's secular system.
The armed forces have ousted four governments since 1960 and such an operation against them would have been unimaginable until recent years.