A Federal Court judge has taken Health Services Union national secretary Kathy Jackson to task over secret emails sent to his chambers by her legal team.

Justice Geoffrey Flick made the surprising revelation at the start of a hearing on an application to have the HSU's east branch put into administration.

The judge told the court that Ms Jackson and her legal team tried to communicate with his associate on the weekend and that such communication was outside the formal processes of the court.

Justice Flick then held up a pile of printed emails and asked what he was meant to do with them.

He said it was a "serious breach" of court processes and queried if action should be taken against Ms Jackson.

The judge also accused one of Ms Jackson's lawyers, Brett Shields, of wasting the court's time by being under prepared.

Outside court, Ms Jackson refused to comment on the developments because the case is before the courts.

A two-week hearing has been set down for the various applications, that were previously going to be heard by two courts.

They include applications by Ms Jackson, HSU acting national president Chris Brown, HSU East boss Peter Mylan and Workplace Relations Minister Bill Shorten.

All want a declaration from the court that both the east branch of the federal HSU and the separate entity HSU East have ceased to function effectively.

Justice Flick has previously told the court it is not his role to hold a Royal Commission, but that someone must look after the union's finances and the interests of HSU members.

But he was quick to knock back a request from one lawyer this morning for the court to break for morning tea.

"We are not the Supreme Court. We do not take morning tea breaks," Justice Flick said.