Dr Haines was hit by a Toyota LandCruiser outside her electorate office in Wangaratta, northern Victoria, on Monday afternoon.
She underwent emergency surgery at The Alfred hospital in Melbourne that night but one of her legs could not be saved.
The 65-year-old remains in a critical but stable condition.
Police on Tuesday charged Tarrawingee man Brendan Nugent, 43, with dangerous driving causing serious harm, intentionally causing serious harm and causing harm to a commonwealth public official.
He will face Wangaratta Magistrates Court on Wednesday morning.
"We do believe this was a deliberate but isolated act," Victoria Police Commissioner Mike Bush told reporters in Melbourne.
Authorities were not ruling out further serious charges, including one of attempted murder, he added.
There was nothing to suggest Nugent was part of the so-called "sovereign citizen" movement, he said, but police were not ruling it out while they trawl the accused's social media.
There was no intelligence to suggest the 43-year-old might carry out the alleged attack, Mr Bush said.
A joint counter-terrorism task force combining Victorian and federal police, and spy agency ASIO are investigating the incident.
"The shocking alleged attack yesterday is what many had been dreading for some time," Australian Federal Police Commissioner Krissy Barrett said.
"I hope that this terrible event, that will forever change the life of the member for Indi and her family, gives our country time to pause and reflect on the growing threats and unlawful behaviour against those who hold a Commonwealth office.
"The current criminal threat environment is febrile."
Mr Bush said additional security preparations were being made in the lead-up to Victoria's November state election.
ASIO, the Australian Federal Police and Home Affairs Department will also brief MPs and senators on security later in the day.
Those bodies have held six such briefings for politicians in 2026, having warned politicians for years about a surge in violent rhetoric and threats against their physical safety.