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Of the remaining 22 people detained earlier, six suspects have been released but could face prosecution later. Questioning of the other 16 people was continuing.
The detentions came five days after a fire sent deadly carbon monoxide coursing through the mine in the western Turkish town of Soma, causing the county's worst ever industrial accident.
The disaster has sparked protests across Turkey, directed at mine owners accused of ignoring safety for profit, and at Prime Minister Tayyip Erdogan's government, seen as too close to industry bosses and insensitive in its response.
An initial report on the possible causes of the accident indicated the fire may have been triggered by coal heating up after it came into contact with the air, Prosecutor Bekir Sahiner told reporters outside the Soma courthouse, rejecting initial reports that a transformer explosion was responsible.
"The crime of which the suspects are accused is causing multiple deaths and injuries due to negligence," he said.
The prosecutor did not identify the three suspects kept in custody but media reports said they were the plant manager and two mine engineers.
Earlier, relatives of those detained joined the crowd of reporters and bystanders outside the courthouse in Soma.
"We know that we have lost 301 loved ones, but we have loved ones inside as well," said the brother of one of the detained engineers. He declined to give his name.
Among those detained was the general manager of the mining company, Soma Madencilik, and the son of the company's owner.
Erdogan has presided over a decade of rapid economic growth but workplace safety standards have failed to keep pace, leaving Turkey with one of the world's worst industrial accident records.
The plant manager has denied negligence at the mine, which was inspected by state officials every six months.
The rescue operation at the coal mine ended on Saturday after the bodies of the last two workers were carried out. They were buried on Sunday.
Mourners cried and prayed beside a line of recently filled graves as one of them was buried in Soma.
Holding their palms open to the sky, around a thousand people said "amen" in unison as a white-bearded imam, or Muslim prayer leader, recited verses.
"My only wish and battle will be to make sure Soma is not forgotten," said a written note, signed "your brother", which was left on one grave along with some flowers.
Ramazan, a worker from a mine near the one where the accident occurred, was among those paying his respects.
"My friend lost half of his family. And for what? To make a living," he said. "Accidents can happen of course, but it's an accident when one person, two people die. When 300 people die, its not an accident anymore."
As the rescue operation wound up, police put Soma on virtual lockdown, setting up checkpoints and detaining dozens of people to enforce a ban on protests in response to clashes on Friday between police and several thousand demonstrators.
Dozens of people were detained on Saturday as hundreds of riot police patrolled the streets while others checked identity cards at three checkpoints on the approach road to Soma.
The checkpoints remained in place on Sunday but those detained, including eight lawyers from the Contemporary Jurists Association, were released by Saturday evening, media reports said.
There were fresh clashes between police and demonstrators in Istanbul and Ankara on Saturday night in protest at the government's handling of the disaster. Protesters again gathered in both cities on Sunday night to voice their anger.
Erdogan's opponents blame the government for privatising leases at previously state-controlled mines, turning them over to politically connected businessmen who they say may have skimped on safety to maximise profit.
His ruling AK Party said the formerly state-run mine at Soma, 480 km (300 miles) southwest of Istanbul, had been inspected 11 times over the past five years. It denied any suggestion of loopholes in mining safety regulations.