Tarrawingee man Brendan Nugent, 43, has been charged with dangerous driving causing serious harm, intentionally causing serious harm and causing harm to a Commonwealth public official over the incident that left Dr Haines fighting for her life.
It's alleged he intentionally struck the 65-year-old MP with his Toyota LandCruiser outside her electorate office in Wangaratta, northern Victoria, on Monday afternoon.
Police have not ruled out further serious charges, including one of attempted murder, Victoria Police Commissioner Mike Bush said on Wednesday.
Law enforcement believe the alleged attack was deliberate, but also an isolated incident.
Dr Haines underwent emergency surgery at The Alfred hospital in Melbourne that night but one of her legs could not be saved.
She remains in a critical but stable condition.
Nugent made a brief appearance in Wangaratta Magistrates Court on Wednesday morning, when he remained quiet in the dock as his lawyer said he was suffering from potential mental health issues and concussion.
He sat staring with dark circles around his eyes and his lips closed.
Nugent's lawyer, Chirag Patel, said his client suffered from a neurological condition, idiopathic transverse myelitis, but had not been diagnosed with any mental health problems.
However, Mr Patel said he had "concerns" about his client's mental health and wanted him to see a medical practitioner.
Court documents show Nugent has also been charged with cultivating and possessing cannabis.
He did not apply for bail and was remanded in custody to face court again in February.
A joint counter-terrorism task force combining Victorian and federal police, and spy agency ASIO continue to investigate the alleged attack.
Establishing if there was a political motivation for the incident would be that probe's first priority, Australian Federal Police Commissioner Krissy Barrett told reporters on Wednesday.
"His motivation for this, what we allege is a deliberate attack, is very much a centre piece of the investigation," she said.
"Our people will continue to explore every element, angle, and avenue to work that out, but at this present point in time I cannot give that information."
Authorities had no specific prior intelligence suggesting Nugent would carry out an attack on Dr Haines.
Victoria Police Commissioner Mike Bush did not rule out further serious charges, including one of attempted murder, being laid against Nugent.
Authorities were also looking into any potential connections to the so-called "sovereign citizen" movement, which espouses anti-government ideology, but Mr Bush added there was currently no evidence to suggest connections.
"We're examining social media associations, talking to witnesses, friends and colleagues," he said.
Whether Nugent had a personal relationship with Dr Haines before the alleged would also be analysed, Mr Bush confirmed.
"We don't understand there's any direct personal contact previously, but we're not ruling that out either, but we're checking full records," he said.
The accused's father, Rod Nugent, and Rod's partner Christine Cunningham on Tuesday revealed they had been friends with Dr Haines for more than 20 years.
The federal police commissioner described the security environment as "febrile" while revealing nearly one person is being charged with targeting federal parliamentarians and high office-holders a week, on average.
The agency will join ASIO and the home affairs department in briefing MPs and senators on Wednesday morning as calls to review politicians' security arrangements grow.
