Colombo Fort magistrate Lanka Jayaratne directed police to detain Admiral Ravindra Wijegunaratne, Chief of the Defence Staff, for allegedly helping the main person acused in the killings escape prosecution.

Chandana Prasad Hettiarachchi, a navy intelligence officer, was accused of leading a hit squad that kidnapped 11 young men between 2008 and 2009 during the final stages of the war.

They are believed to have been murdered while being illegally held by the navy. Their bodies were never found.

Hettiarachchi was arrested earlier this month in Colombo after a months-long manhunt that saw an alert issued worldwide.

"There is evidence against Admiral Wijegunaratne's role in allowing the accused to evade arrest," Sri Lanka's Criminal Investigations Department told the magistrate.

D.K.P. Dissanayake, at the time a spokesman for the navy, is also suspected of involvement. He was arrested last year and is currently on bail.

Police have told the court that Hettiarachchi was also wanted in connection with the 2006 murder of Tamil lawmaker Nadarajah Raviraj.

There have been persistent allegations that senior military personnel and regime figures loyal to then-president Mahinda Rajapakse were responsible for a number of high-profile murders.

Several military intelligence officers are facing prosecution in connection with the assassination of a prominent newspaper editor and for orchestrating attacks on other journalists and dissidents during Rajapakse's rule that ended in January 2015.

Rajapakse himself was questioned two weeks ago in relation to the abduction and torture of a newspaper journalist in 2008.

The former strongman, and several members of his family, are also being investigated for large-scale financial fraud and murder during his decade as president.

Troops crushed Tamil separatists known as the Tamil Tigers in 2009, ending the decades-long civil war.

But the final days of the government offensive, spearheaded by Rajapakse, were marked by allegations of major rights violations.

A former UN official has claimed that up to 40,000 civilians may have been killed in the final stages of the war.