They were among 25 people detained on Sunday, including several mining company officials.
Soma mine explosion and fire on Tuesday sent carbon monoxide gas into the mine’s tunnels, claiming 301 lives.
It was Turkey’s worst-ever mining disaster and sparked protests against the government and mine operators.
The three facing charges are also accused of negligence, AP news agency reports.
Public prosecutor Bekir Sahiner said that one of the 25 arrested was the mine’s operations manager.
The manager, Akin Celik, has previously denied any negligence.
Turkey’s Dogan news agency has also said general manager Ramazan Dogru was among those arrested.
It is not yet clear if either of the men faces charges.
Six of those arrested on Sunday have now been released, the prosecutor said.
Initial reports suggest that the disaster could have been caused by coal in the mine overheating.
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