The move came a week after the government overcame a no-confidence vote over its handling of the deadly 2023 train disaster, which has again sparked protests in Athens and other cities since January.
The foreign and defence ministers were unchanged.
The two trains had travelled towards each other on the same track for miles without triggering any alarms. It was blamed on faulty equipment and human error.
A protest held on the second anniversary of the tragedy drew hundreds of thousands of people nationwide.
An experts' report funded by the victims' families has claimed the freight train was carrying an illegal and unreported load of explosive chemicals, which contributed to the high death toll.
The train's Italian-owned operator, Hellenic Train, has denied knowledge of any illegal cargo.
More than 50 percent of Greeks want early elections, and more than 65 percent of ruling party voters believe government officials should be put on trial for the accident, a poll for Star TV found earlier this month.
She said the phones of Mitsotakis and other senior officials should be examined to determine whether “orders were given” to investigators to “destroy and conceal evidence” at the collision site.
A previous parliamentary committee investigating the tragedy concluded last March without assigning blame to senior politicians.
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