Former Salvation Army worker Joshua Kaluvia escaped from jail on Manus Island on March 28.
He was one of two men accused of killing Iranian asylum seeker Reza Barati in February 2014 during a riot, the ABC reported.
Kaluvia was meant to appear in court in the town of Lorengau on Manus Island to continue the trial, but the court was told he had escaped from remand at the Lorengau prison.
Police on Manus Island said prison staff took a week to tell them Kaluvia had escaped.
Officers have said Kaluvia has been recaptured, but have not yet provided details.
Trial judge Nicholas Kirrowom issued a warrant for Kaluvia to be recaptured and to reappear in court by April 18.
Kaluvia had pleaded not guilty and had complained about the standard of his defence during the trial last year.
Police had struggled to find Kaluvia when he was first named as a suspect in the case after his friends initially told them he was dead.
He was later arrested on the island of New Britain.
A Senate inquiry in December 2014 found the cause of the riot - in which 23-year-old Barati died - to be a failure to process asylum seeker claims, stating the violence was "eminently foreseeable".
It also found that the Australian Government failed in its duty to protect asylum seekers, including Barati.
About 70 asylum seekers were injured during the riot, some seriously, in what the Government described as a "disturbance" on Manus Island.
Then-Immigration Minister Scott Morrison accused Labor and the Greens at the time of using the report "as a blatant attempt to whitewash their own failures in government".