Police discovered the shallow grave in suburban Bethania south of Brisbane on Monday after a tip-off.
The body was underneath the cubby house in a backyard that was "a bit of a mess", Detective Inspector Ian Galpin said.
"Located in a box in what I will call a shallow grave, police located human remains," he told reporters on Tuesday.
The remains are believed to be of Chad Steven Bishop who was 46 when last seen in early March 2022.
Police determined the home's two residents were not involved with the body's burial.
Instead, they arrested Courtenay Williams, 52, and Carlie Rochelle Mordue, 45, and charged the duo with murder and interfering with a corpse.
The Bethania carpenter and Windaroo sales assistant will remain in custody after their charges were briefly mentioned in Brisbane Magistrates Court on Tuesday.
Det Insp Galpin said Mr Bishop's suspected remains could have been buried at the Bethania property more than four years ago.
"There will be an autopsy conducted in the coming days to establish the exact cause of death, and identification of the body will occur in due course," he said.
Mr Bishop's family has been informed of the body discovery.
"The family understand that formal identification is yet to occur but they're very grateful for the ongoing investigation," the detective said.
"We continue to keep them updated and we'll continue to do that, and we continue to support the family in any way that we can."
Mr Bishop and the arrested pair were known to each other but police did not comment on a possible motive or whether other people were being sought.
Police allege Williams and Mordue murdered Mr Bishop in a Beenleigh townhouse on or about March 2, 2022, according to court documents.
Williams and Mordue were not required to appear in court on Tuesday.
A three-week adjournment was sought by Williams's solicitor Madeline Jacks on Tuesday.
"There's no bail application given the nature of the charges," Ms Jacks said.
Defendants in Queensland facing charges carrying a possible life sentence can only apply for bail in the Supreme Court.
Mordue's solicitor Kate Bassett also sought an adjournment for her client.
Magistrate Belinda Merrin adjourned both cases to September 7 at Brisbane Magistrates Court.
Williams and Mordue were both remanded in custody to appear by videolink at the next mention.
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