Controversial union boss John Setka and his estranged wife have fronted court after Emma Walters was charged over an alleged plot to kill him.

The pair arrived separately at Melbourne Magistrates Court on Thursday on a matter unrelated to the charges against Ms Walters.

On Wednesday night she was charged over plotting to acquire a firearm and murder her husband. She denies the allegation.

Mr Setka is Victorian secretary of the Construction, Forestry, Mining and Energy Union.

Ms Walters is a former lawyer and they have two children together.

Ms Walters was interviewed by police on Wednesday and charged with incitement to commit conspiracy to murder the construction boss.

Victoria Police confirmed in a statement that a woman had been charged “after she allegedly attempted to acquire a firearm and made threats to kill a man earlier this month”.

“Investigators executed a search warrant at a residential address in Footscray on Wednesday where they seized a mobile phone,” the statement said.

It said a 46-year-old Footscray woman was charged with incitement to commit conspiracy to murder, incitement to acquire a firearm and making threats to kill.

When contacted, Ms Walters told The Age newspaper: “I deny that allegation”.

“I’ve been handcuffed today, I’ve dealt with the allegations that have been put to me,” she said, maintaining she had acted only to protect herself.

Mr Setka and Ms Walters have been involved in a long-running legal battle involving allegations he committed acts of domestic violence and breached intervention orders.

Ms Walters is suing the Victorian government over claims police failed to protect her.

Mr Setka has denied allegations of domestic violence but in 2019 was convicted of harassing Walters and breaching the orders.

Ms Walters has been bailed to face Melbourne Magistrates’ Court on April 5.