The Commission issued the direction to the Station House Officer of Varapuzha in Ernakulam district, a press release said.
The amount should be deducted from the Sub-Inspector's salary, the commission said in an order to the state DGP and Ernakulam rural SP.
The commission chairperson Shobha Koshy also directed that a case should be registered against sub-inspector Sharon C S and the matter be probed.
The boy, whose parents are separated, was summoned to the police station and allegedly beaten up after he refused to go with his mother, the release stated, adding the commission had suo motu launched proceedings on the basis of media reports.
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