A checkpoint began operating at a Chiltern rest stop on Friday morning, with all vehicles passing through the site being scanned.

The Victorian school holidays end tomorrow, and Wodonga Inspector Paul Hargreaves said police had a particular focus on checking NSW vehicles.

"The public can expect to see us in various locations in coming days to identify interstate and returning Victorians from interstate," he said.

"We've been pleased with compliance to date, but we have had some penalties issued.

"Our intent is to make sure that those who are returning have got the correct permits and are complying with the Chief Health Officer's directions as they move into Victoria."

Police had been focusing on vehicles using the Murray Valley Highway near the Bandiana army bases in recent weeks.

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The Chiltern site will be used for several days before moving, and police continue to check vehicles on other roads.

Border residents can continue to use their licences instead of permits, while those who need permits are urged to have them accessible.

The freeway site was chosen to avoid causing excessive delays to local traffic.

"We're trying to do our best to strike the right balance," Inspector Hargreaves said.

"However if people think they're going to return or try to return against the Chief Health Officer's instructions, the fines are substantial and we will not hesitate to use them when we see a blatant disregard of those laws.

"If there are multiple people in a vehicle, there will be multiple penalty notices issued."

He asked drivers to be patient at the site.

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