Dr Haines' husband Phil Haines confirmed the member for Indi's left leg was amputated on Monday and medical staff were unable to save her right leg on Wednesday afternoon.
"But the good news in all this is Helen is alive and she's stable," Mr Haines told reporters inside The Alfred Hospital in Melbourne.
"We are grateful and thankful that, at this stage, both her heart and her mind are in good shape."
The incident comes just weeks before the couple were due to celebrate their 40th wedding anniversary.
"Thanks to (the) many people who have been incredibly supportive of our family the last two days since this horrendous incident took place ... we will need that over the next few days and beyond," Mr Haines said.
Governor-General Sam Mostyn, a close friend to Dr Haines, highlighted the "extraordinary" character of the bystanders, including barber Ricky Jeffries, who was one of the first on the scene.
She said she had discussed the importance of civil debate and civic engagement with Dr Haines during a meeting in her electorate earlier in October.
"Australians have good hearts, great hearts ... we don't have to all agree, but we can wrestle the issue, not the person, just as Helen has done throughout her time in Parliament."
Ms Mostyn said she has provided King Charles III regular updates on the "shocking" situation.
The man accused of deliberately running down the MP will remain behind bars for months while the alleged attack is investigated by counter-terrorism authorities.
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 which 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.
During Nugent's brief court appearance on Wednesday, his lawyer Chirag Patel said the man suffered a rare neurological condition called idiopathic transverse myelitis, caused by a swollen spinal chord, as well as concussion.
He had not being diagnosed with mental health problems, but Mr Patel said he had concerns about his client's psychological wellbeing and wanted him to see a medical practitioner.
Nugent sat quietly in the dock in the packed courtroom, his mouth shut and dark circles around his eyes.
Cultivating and possessing marijuana were among the charges on his rap sheet, court documents show.
Nugent did not apply for bail and was remanded in custody to face court again in February.
Law enforcement have not ruled out further charges, including attempted murder, Victoria Police Commissioner Mike Bush said on Wednesday.
Nugent's former primary school teacher on Wednesday told AAP the accused attacker had been a good kid, but probably had deeper-seated issues.
Jacquie, who preferred not to give her surname, described him as withdrawn, but "beautiful, like most of the kids were".
Mr Bush said authorities were also investigating any prior personal personal relationship between Dr Haines and Nugent.
"We're examining social media associations, talking to witnesses, friends and colleagues," the police commissioner 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, calling the alleged attack "devastating and unfathomable".
Immediately after she was hit by the large off-roader, Dr Haines was still talking and thanking bystanders who intervened, eyewitnesses have reported.
Jacob Evans and Jacklyn Black, who were visiting Wangaratta from Melbourne, rushed to the MP's side on Monday despite not knowing her "from a bar of soap", they told AAP.
"She was thanking us and calling us beautiful people," Ms Black said.
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