The Fair Work Building and Construction watchdog has launched a new case against two members of the Construction, Forestry, Mining and Energy Union Victorian branch, after allegations of thuggish behaviour.

Members of the powerful construction union allegedly told one company it was on a “hit list” and set to suffer industrial strife - payback for reporting illegal site visits to police.

“Trust me, you don't want to be the dog who calls the cops on a union official,” CFMEU organiser Stephen Long allegedly told a site manager in Cheltenham, according to Fairfax Media reports.

"We will have 500 blokes here on site tomorrow. We won't sign an EBA with you guys next year, your wages will drop, you blokes will be on nothing.”

The new Fair Work lawsuit implicates Mr Long and union colleague Drew McDonald, alleging that he told the company “you're on the top of our hit list” after it asked them to comply with right-of-entry laws.

“Who's going to stop me? All this s--t is going to blow over in a few weeks, but we won't forget this low act,” Mr Long allegedly said after the company mentioned notifying police of his entering its $20 million Cheltenham worksite.

Documents to be filed in the Federal Court will allege Mr Long entered the site anyway, and spoke with form-workers and concrete workers.

The Fairfax reports say he then returned to the front gate and asked the site manager if he had called the police.

When the site manager confirmed that he had, Mr Long allegedly threatened retaliation including refusing to sign another enterprise agreement.

It is alleged that Mr Long and Mr McDonald also declined to provide their right-of-entry permits at a $22 million cold storage project in Laverton North, which managed by the same contractor.

If union officials want to enter a site they must hold a valid federal right-of-entry permit and provide 24 hours' notice, and must show their permit upon request.

Fair Work Building and Construction director Nigel Hadgkiss said the allegation involved serious matters that warranted a closer look.

“Threatening or intimidating workers will not be tolerated,” Mr Hadgkiss said.

“I find reports of threats made in response to a simple request to comply with the law particularly concerning.”