Senior sources have told the Herald that gardai think that Murphy and his pal travelled to Northern Ireland from their hideaway in Amsterdam a number of weeks ago.
"Gardai know that Murphy and his friend left Amsterdam together; the belief is that both men then travelled to the North.
"Gardai have asked the PSNI to look out for Murphy. He will be devastated that his mate is now locked up."
His friend, who is from Co Roscommon, has lived with Murphy for more than a year in his Amsterdam hide-out and was even caught on camera with the sex beast by a film crew in the Dutch city last year.
As a convicted sex offender, he has to inform gardai of his new address when he leaves the country or moves within Ireland. He failed to do so, and as a result, a EAW was issued by gardai. The sex offender, who cannot be named, was brought before Belfast Laganside Court.
He was remanded in custody and will appear in court again on February 1. He is expected to be extradited to the Republic.
The rapist formed a close bond with Murphy while both were imprisoned at Dublin's Arbour Hill jail.
Murphy is the chief suspect in the disappearances of Annie McCarrick (26), Jo Jo Dullard (21) and Deirdre Jacob (18), who all vanished in Leinster in the years before he kidnapped and raped a Co Carlow woman.
Earlier this month, cold-case detectives conducted fresh searches for the remains of Deirdre Jacob. It is understood that five locations have been drawn up by officers investigating her disappearance.
Ms Jacob is thought to have been snatched near her home in Newbridge in July 1998.
Search teams and garda divers conducted a secret trawl of a lake in Co Wicklow last month, but nothing was found.
Since Murphy's conviction and subsequent imprisonment, no other women have disappeared in such circumstances.
Gardai set up Operation Trace to try to solve the mystery of the missing women: their primary target was Murphy.