Gottfrid Svartholm Warg was arrested on cybercrime allegations Thursday after a request from Sweden, local media said.
Svartholm Warg's final destination had not been decided as he was due to be expelled under immigration law, police spokesman Kirth Chantharith told dpa.
Sweden and Cambodia do not have an extradition agreement, he said.
In 2009, Svartholm Warg was sentenced to 12 months in prison by a Swedish court for illegally sharing copyrighted content.
The sentences of three Pirate Bay colleagues were reduced by varying degrees in a 2010 appeal, but Svartholm Warg did not attend the hearing and his original sentence stands.
The Pirate Bay co-founder was known to be living above a popular American bar in Phnom Penh's riverside area prior to last week's arrest.
He had been in the Cambodian capital for four years, according to popular local website Khmer440.com.
A representative from the Swedish embassy in Phnom Penh who met with Svartholm Warg last week said Tuesday that he was "fine, considering the circumstances." The Pirate Bay was started in 2003, according to its website, which states it does not store copyrighted or illegal material.