The disappearance of the urn- believed to contain hair, teeth and bones of Buddha- and several small statues came to light in December and prompted an outcry in the Buddhist-majority country.
Authorities said they found the relics during a raid yesterday at a house in the southern province of Takeo, about 130 kilometres away from the shrine in the former royal city of Udong.
"Everything is still in the urn," national police spokesman Kirt Chantharith told AFP.
Five guards at the shrine were also arrested in December.
The relics are believed to have been brought from Sri Lanka to Cambodia in the 1950s to celebrate 2500 years since Buddha's birth.
In 2002, then King Norodom Sihanouk moved the relics from the capital Phnom Penh to Udong, some 45 kilometres from Phnom Penh- in a ceremony attended by tens of thousands of people.