The company has warned that staff shortages could affect AGL's ability to generate energy at up to three of its four units at the Latrobe Valley plant.

Days after the Fair Work Commission granted AGL's bid to terminate a workplace agreement with the CFMEU at the Loy Yang A power plant, the company on Friday accused the union of organising unauthorised industrial action by telling members to refuse requests for overtime.

Last week one of the four generation units at Loy Yang – one of Victoria's largest power generators – was shut down due to a fault, and overtime shifts were needed to fix it, but not enough staff were available to fill the shifts.

AGL said that as a result of few staff being available for overtime it had been unable to return the unit to service. The shortage also caused "some periods of closure" of a second unit on Friday.

"AGL Loy Yang made the application as a result of having to take two of four units offline, and potentially a third unit, due to staff not making themselves available for work," a spokeswoman said.

"AGL Loy Yang's concern is having units down could present an issue where supply of electricity to the Victorian community becomes compromised, especially as industry starts up again after the holiday break and the hot weather continues."

The company argues that staff not making themselves available for work is unprotected action in the form of overtime bans and increased absenteeism orchestrated by the union.

But Fair Work Commissioner Julius Roe found there was no evidence that workers were refusing overtime, as they are entitled to under their agreement, as part of industrial action.

The relationship between union and management soured last week after AGL successfully terminated a workplace agreement, which workers fear will result in their pay being slashed by up to two-thirds.

Conditions would also be lost and more than a third of the workforce may resign to protect their defined benefit superannuation scheme, the union says.

While Mr Roe found there was "good reason to be suspicious" that the difficulties AGL has in being able to get sufficient staff to work overtime is a response to the decision to terminate the agreement, he found no evidence that there was an industrial campaign.

"In my view there is inadequate evidence to establish that any employee has unreasonably refused to work overtime," Mr Roe said.

CFMEU, mining and energy division Victorian secretary Geoff Dyke said AGL's action was insulting, because on some of the shifts that AGL complained about workers did turn up, just not enough.

"To suggest there is an overtime ban when seven out of eight [staff] are turning up is ludicrous," Mr Dyke said.

"AGL's agenda is to smash the union; they want to dictate everything has been the problem in bargaining, they have not negotiated in good faith."

Mr Dyke said the action had further eroded the relationship between staff and employer. Before Christmas strike action at the plant was averted after the Andrews government intervened.

Energy Minister Lily D'Ambrosio said the government had been advised by Australian Energy Market Operator that there was sufficient supply to meet Victoria's needs.