Deputy Inspector General of Police Lalith Jayasinghe, who was the in-charge of the Jaffna division, landed in the police net for helping the accused flee the police custody, police's Crime Investigation Department (CID) said.
The rape and murder of 18-year-old student Sivaloganathan Vithya in Jaffna in 2015 had triggered widespread public anger and protests with people demonstrating to bring the accused to justice.
Protesters had accused the police of shielding the accused in Tamil-dominated northern province.
Sri Lanka's human rights record particularly over the impunity enjoyed by law enforcement officers has been the subject of international condemnation.
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The UN Human Rights Council has called for an international investigation into the alleged war crimes in Sri Lanka during the military conflict with the LTTE that ended in 2009.
Sri Lanka is averse to setting up of an international hybrid court with local and foreign judges to investigate the alleged war crimes committed by the government troops and the LTTE in the last phase of the conflict.
Relatives of the missing Tamil people allege that the Lankan state - particularly its army, navy and police - were behind most of the disappearances.