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Greg Lynn, from Caroline Springs, was arrested on Monday by specialist police at a remote campsite in Arbuckle Junction, 280km northeast of Melbourne. He will face Sale Magistrates Court on Friday.
Police and forensic specialists are now scouring Victoria's Great Alpine region for Mr Hill and Ms Clay's remains, after a crime scene was established in the area on Thursday.
"We've located a specific area and we will be establishing a search parameter in the coming days," Assistant Commissioner Bob Hill told reporters on Thursday night.
"We are hopeful that we will locate the remains of Mr Hill and Ms Clay... and provide closure to their families.
"This investigation is far from over."
He declined to give the exact location of the crime scene, due to significant community and media interest.
Asst Comm Hill confirmed no one else was being sought for the murders and called for anyone with information on a trailer to come forward.
He said the silver and blue-coloured trailer with off road wheels, which was attached to a blue four-wheel-drive, was sold on Gumtree between March and July 2020.
Police would also like to speak to anyone who was in the Wonnangatta area around that time, including "campers, 4x4 day trippers, hunters, fishermen or trail bike riders", regardless of whether they saw or heard anything.
Mr Lynn's Nissan Patrol four-wheel-drive has also been seized.
Asst Comm Hill said the arrest came after police adopted "unique investigative techniques" with support from specialist services.
"It is one of the most significant investigations we've undertaken in recent years," he said.
"There's been hundreds of people spoken to, hundreds of vehicles that have been eliminated, in excess of 1000 information reports are on the system."
Mr Hill and Ms Clay were last heard from on March 20, 2020 while camping in the Victorian Alps.
Mr Hill left his Drouin home on March 19 and picked up Ms Clay from her home in Pakenham in his white Toyota LandCruiser.
On March 20, Mr Hill - an experienced outdoorsman - made a call via high-frequency radio saying he was at Wonnangatta Valley.
Ms Clay, a former Victorian Country Women's Association president, told friends she was heading away and expected to return home on March 28 or 29.
Investigators were told the couple were camping together at Wonnangatta River near the Wonnangatta camping ground.
Campers found Mr Hill's car destroyed by fire at their campsite near Dry River Creek Track on March 21.