Rev Basil John Hutsko told police he was attacked on Monday morning inside the St Michaels Byzantine Catholic Church in Merrillville.
Police Chief Joseph Petruch told CNN the attacker "grabbed him by the neck threw him down on the floor and immediately started slamming his head against the floor".
He added that the assailant, who left Hutsko unconscious, yelled "This is for all the little kids" during the assault.
The attack follows the recent grand jury report in Pennsylvania that detailed decades of abuse of children by more than 300 priests in the US state.
A fellow priest said Hutsko has never been accused of sex abuse.
"He's a very dedicated priest and hardworking and in good standing, it's just a random act [on] an innocent priest," Rev Thomas Loya explained.
The police chief added: "I have enough there to say it's a hate crime."
No one's been arrested so far in the case.
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