Workers at the Australian Synchrotron in Melbourne say they were threatened with "impacts" on their promotions and bonus prospects if they went ahead with protected industrial action as part of a pay dispute.

But the Synchrotron's management categorically denies the claims by workplace union Professionals Australia with the union in turn standing by its members' account and demanding a full explanation be provided to all staff.

With the Synchrotron's management insisting it has done nothing wrong and rebuffing the union demands, a meeting on Thursday between the two sides failed to produce a peace agreement.

The trouble started on July 14 when the Synchrotron's scientists and researchers, who carry out world-leading experiments with high speed electrons, were gathered together to talk about their no-vote to a wage offer and the decision to take protected industrial action.

The union alleges that a senior manager told the meeting that stop-work actions would mean the loss of wages and also mentioned an upcoming bonus and promotions rounds with workers going away with the impression that their bonuses and promotions prospects were under a cloud.

Synchrotron says the bonus and promotions were mentioned but in a completely unrelated context and managers are bewildered that one of them is being accused of making veiled threats.

But the union's Victorian director Sharelle Herrington says her members were in no doubt they were being threatened.

"Some of our members … took this as a direct threat that ongoing protected industrial action would have a detrimental impact upon their promotion and bonus entitlements as prescribed by the enterprise agreement," Ms Herrington wrote in a letter of complaint.

"Other members…drew an inference that ongoing protected industrial action would have a detrimental impact upon the aforesaid entitlements.

"Our members felt that their lawful entitlements as prescribed by the enterprise agreement would or could be in jeopardy if they continued their protected industrial action."

The ill feeling was heightened, according to the union, when management asked for the names of the union members who complained about the July 14 meeting.

But the Synchrotron's head of corporate service, Dr Dean Morris, emphatically rejected the notion that any of his staff were threatened.

In an email sent to Ms Herrington on July 17 in a bid to defuse the row, Dr Morris denied that any threat was made.

"No threat was made, implicitly or explicitly, that staff taking protected industrial action would be adversely affected in the upcoming bonus round," the manager wrote.

"We respect and support the right of our employees to take protected industrial action.

"No employee taking protected industrial action will be harassed, intimidated or discriminated against in any way."

Dr Morris asked the union official to show his email to any Professionals Australia members who had concerns.

But the union remains unhappy and has not backed away from its demand for an all-staff bulletin clarifying the position, with the Synchrotron adamant it will not happen.

Ms Herrington said she would not rule out action in Fair Work Australia if the two parties could not reach a negotiated settlement.