The union heavyweight was arrested on Wednesday morning by state and federal police at his Footscray home, in Melbourne's inner west, where officers seized a phone and an iPad.
Police allege Setka sent threatening, offensive and abusive emails to CFMEU administrator Mark Irving following a production notice sent on October 27 and a follow-up letter sent the next day.
The 61-year-old has been charged with seven counts of using a communications device to menace, harass and offend.
He was bailed to appear at Melbourne Magistrates Court on January 30.
Setka quit after 12 years as head of the Construction, Forestry, Maritime and Energy Union in Victoria in 2024 following a Nine investigation into criminal links within the construction industry.
The company's reporting alleged major Victorian and NSW construction projects had been infiltrated by underworld figures and bikies acting as union delegates.
Setka said the allegations against the union were false but said he would step down to stop the barrage of stories.
The construction and general division of the union, including all its state branches, were placed into administration in mid-2024 in response to allegations of serious misconduct, corruption and violence.
Taskforce Hawk, which played a role in Setka's arrest, was established in July 2024 as Operation Hawk to investigate allegations of serious and violent criminal behaviour linked to the construction industry.
It aims to target organised crime within the sector, focusing on individuals employed within the construction industry who have known links to outlaw motorcycle gangs.
The taskforce investigates all criminal behaviour linked to the industry, whether it be extortion, arson, serious violent offending or threatening and harassing communications, Assistant Commissioner Martin O'Brien said.
"We will not tolerate behaviour that aims to intimidate and harass people who simply want to be able to go to work and perform their job to the best of their ability," he said.
Setka garnered a dedicated following and significant influence during his time in the CFMEU role while also being linked to a string of controversies.
His union leadership came into question in 2019 when then-opposition leader Anthony Albanese moved to expel him from the Labor Party over accusations he said family violence campaigner Rosie Batty's advocacy had led to men having fewer rights.
Setka rejected the allegations and fought his expulsion from the party in court but was cast out months after being convicted of harassing his now-estranged wife.
He is also facing legal action by the Fair Work Ombudsman over allegations he tried to coerce the AFL into sacking its chief umpire.
The ombudsman alleged Setka intended to coerce the AFL into dismissing Stephen McBurney, the former head of the now-defunct Australian Building and Construction Commission.
Setka was referred to the police in September 2024 for appearing at government building sites to verbally attack the Victorian and federal governments, but he did not face charges over the visits.
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