The "militant" CFMEU has been fined almost $100,000 for banning contractors from a Victorian building site because they hadn't paid their membership fees but a judge isn't confident the penalty will stop the union doing it again.

Union delegate Andrew Harisiou breached the Fair Work Act when he prevented two catering equipment company employees from working on a Werribee shopping centre expansion in August 2015, the Federal Court found on Monday.

The CFMEU was ordered to pay $90,000 and Harisiou $8000 after the men were banned because they weren’t union members or were behind on membership payments.

But Federal Court Justice Richard Tracey doubts whether any penalty will prevent the union from offending again.

He told the court the CFMEU had been penalised more than 120 times for breaching the Fair Work Act since 2000.

“Having regard to the history of offending by the CFMEU … it may be doubted that any penalty falling within the available range for contraventions of the kind presently under consideration would be ‘sufficiently high to deter repetition’,” Justice Tracey said.

According to agreed facts tendered in court, Harisiou told two Action Commercial Catering Equipment employees words to the effect of “you can’t get on site … if you’re not financial, you’re not getting on the site”.

“If you’re not part of the union, you’re not allowed on this site,” Harisiou also said.

Federal Employment Minister Michaelia Cash said the “militant, corrupt” union would continue to deliberately break the law unless penalties are raised.

“Justice Tracey is the second judge in two weeks to express concern that penalties that can be imposed by the courts are too small to act as a deterrent,” Ms Cash said in a statement.

The Australian Building and Construction Commission said no one has the right to impede on a worker’s rights.

“This is a reminder to employers and union delegates alike that every worker has a right to choose whether or not they want to join a union,” Acting ABCC Commissioner Cathy Cato said.

One of the men booted from the site was later allowed to return after paying the union more than $150, court documents said.

Justice Tracey labelled Harisiou’s conduct “deliberate and wilful”.

“He arrogated to himself the right to determine who would and would not be permitted to work on the site,” the judge said.

“In doing so he undermined provisions of the Act which were designed to ensure that workers enjoyed freedom of association in the workplace.”

By Christopher Talbot and Georgie Moore