Victorian supermarket shelves could be empty and fresh food could rot at sea if a union-backed blockade at the Port of Melbourne does not end soon, the Victorian Transport Association has warned.

About 50 workers from the Maritime Union of Australia have shut down the Victoria International Container Terminal (VICT) over the alleged treatment of one of its members.

The dispute has been ongoing for 10 days, forcing precious cargo to be diverted to Adelaide and then taken by road to Melbourne.

"There are goods coming directly into the shelves, there are goods being bought left right and centre," said the association's chief executive, Peter Anderson.

"Unfortunately the supply chain will be disrupted by this action."

Accusations of company bullying and intimidation

The long-running dispute between the union and the VICT came to a head when an audit revealed that 22 workers did not have a Maritime Security Identification card, which lets workers into secure areas.

According to the union, the one worker who had taken the company to Fair Work had his employment terminated.

Wharfies blockaded the Port of Melbourne after a worker was denied shifts for not having a permit. ( AAP: Luis Enrique Ascui )

"This is the one person who had gone to the courts to raise the issue of bullying and intimidation and for that reason they sacked him and him only," said the union's Will Tracey.

"It's the company holding the community here to ransom in terms of treating one worker differently from the other 21 who identified without a permit."

The worker in question has a criminal record and has held a Maritime Security Identification card before.

Victorians being 'held to ransom'

But Mr Anderson said the workers' record makes him ineligible to work at the docks.

"The union want to then force the company to take this worker on," Mr Anderson said.

"It's now the company and all of Victoria through the supply chain process that's being held to ransom."

The company is accusing unionists of holding Victorians to ransom. ( AAP: Luis Enrique Ascui )

But Mr Tracey said other workers have just applied for discretionary permits after getting a police clearance.

"We probably have two or three people a week run into that sort of problems with their permits," Mr Tracey said.

The union wants the company to withdraw its letter of termination and give the man shifts when he gets his permit back.

"This company could fix this dispute right now, in the next 10 minutes," he said.