Identities of the deceased could not be known immediately.
Witnesses said Khulna bound Mohanagar Express train crushed a private car at the level crossing at Noapara bridge area near Dhaka-Khulna highway in the afternoon.
The accident killed two on the spot, later, another died after being taken to the hospital, said Officer-in-Charge of Abhaynagar Police Station Tajul Islam.
The injured were admitted to the Khulna Medical College Hospital, OC said.
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