Police will allege an armed robber confessed to the incident as they continue to try to find the gun involved.
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Jarrod Medcraft, 24, remains in custody after appearing in Albury Local Court on Thursday.
He had been dealt with in the court on Wednesday after being arrested in Wodonga a day earlier as part of an investigation into two service station robberies involving a gun on Saturday.
The United petrol station on McKoy Street, Wodonga, and the BP on Travelstop Way in Lavington were targeted.
Detective Chief Inspector Mick Stoltenberg said Albury police had had a breakthrough while he was still in their custody, which led to him being charged with the Lavington BP armed robbery.
He allegedly destroyed and disposed of distinctive clothing used in the incidents, and faces a charge of evidence tampering.
The firearm and a motorbike allegedly used in the incidents haven't been recovered, nor have stolen cash or cigarettes.
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"The most concerning and alarming thing is there is still a firearm in the community," Detective Chief Inspector Stoltenberg said.
But he said it was "good news for the Border community" that the arrest had been made.
"It's a good breakthrough," the detective said.
"I'm pretty confident both sides of the border are going to be satisfied and very happy with the outcome."
There was no evidence other people were involved.
Police are investigating Medcraft's alleged motivation.
Medcraft did not apply for bail on Thursday and will return to court on August 17.
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