A Turkish court on Friday handed down 20-year prison terms to three former generals accused of plotting to overthrow the government in 2003.

The three chief suspects in the trial, including alleged mastermind Cetin Dogan, former commander of the First Army, were initially given life sentences, which were commuted on the grounds that the alleged plot failed.

They have the right to appeal the landmark verdict, the first from a series of trials over alleged plots by the once-dominant Turkish army, which has been responsible for four coups in half a century.

Dubbed the "Sledgehammer" trial after a 2003 military exercise, it was the first such case tried in a civilian court.

The two-year-long trial of 365 defendants including retired and active army officers wrapped up at the court in Silivri, near Istanbul, on Friday with the final testimonies of the last suspects accused of plotting against the ruling Justice and Development Party (AKP).

Only 34 defendants were acquitted.

Seventy-eight officers were sentenced to 18 years in prison and 246 to 16 years. Among them, the court commuted the sentences of 28 officers to 12 years in prison.

Prime Minister Recep Tayyip Erdogan, whose government was targeted by the alleged conspiracy, said in televised comments that the trial was not yet finalised, recalling the appeal process.

"We need to follow and see the decision of the supreme court of appeals. We all expect a rightful decision to come out from there," Erdogan told reporters in Ankara.

The Sledgehammer trial, which began in December 2010, was unprecedented in its offensive against the military, seen as the guardians of Turkey's secular political system founded by Mustafa Kemal Ataturk. But Turkey is a Muslim-majority country.

"This verdict will be thrown into the trash of our judicial history," Dogan's wife Nilgun told reporters in Silivri.

Prosecutors have demanded up to 20 years in prison for the army officers in the case, which concerns alleged army plans to bomb historic mosques in Istanbul and spark conflict with neighbouring Greece to facilitate a military coup.

The defendants argued that the alleged plot was a military exercise regularly held by the army, and questioned the authenticity of some documents presented as evidence.

Amnesty International said in a statement released in Turkish that the court ruling "highlights the importance that those responsible for rights violations are delivered to justice".

If the alleged coup plot had succeeded, it stressed, many citizens would have died and a series of human rights violations would have taken place.

"It is important that such kind of allegations are effectively investigated for the protection of human rights and those responsible are delivered to justice as a result of a fair trial process," the statement said.

Pro-government circles have praised the trial as a step toward democracy, while critics have branded it a witch-hunt to silence opposition.

The Turkish army overthrew three governments in 1960, 1971 and 1980.

In 1997, it pressured an Islamic-leaning prime minister, Necmettin Erbakan, into stepping down. Erbakan was the political mentor of current Prime Minister Recep Tayyip Erdogan.

The families of the suspects, who were present in the courtroom, chanted republican songs and shouted "Turkey is proud of you" in a show of solidarity. The suspects saluted the crowd in return.

Some of the defence lawyers also joined the protest.

Hundreds of suspects, including army officers, journalists and lawmakers, are being tried separately over their alleged roles in plots to topple the Islamic-rooted government.