The doctor gave evidence on Friday at a coronial inquest into the death in custody of Wayne Hunt at Darwin Correctional Centre on August 29, 2024.
She also raised concerns a surge in prisoner numbers and shortages of prison guards had made the prison less safe for detainees and a trying place to work.
The inquest has been told Mr Hunt became combative after his seizure and struggled against prison guards who roughly handled him, pinning him down on a mattress, handcuffing him and putting him in a spit hood.
He was bundled off in a wheelchair to the medical unit but instead of being given a full medical check, he was left naked on the floor of an "at-risk" cell.
The 56-year-old was found unresponsive in the cell the next morning and rushed to hospital, where he died two days later.
The doctor, whose identity has been suppressed by Coroner Elisabeth Armitage, was near the end of her shift on the evening Mr Hunt had his seizure.
She did not see him in person but issued instructions to a nurse on his treatment, including sedatives to calm him.
The doctor told the inquest she looked down the corridor to see Mr Hunt being taken to an at-risk cell, thinking it "not right" that someone who had a seizure was not going to a resuscitation room for a full medical check.
She assumed Mr Hunt would soon be moved to the resuscitation room as all "code blue" medical emergency cases were taken there.
The doctor said Mr Hunt should not have been put in a spit hood, and if she had known that and the rough way guards had treated him, she would have intervened and sought his transfer to the resuscitation room.
"In retrospect, I would have walked down that hallway," she tearfully told the inquest.
The doctor said medical staff often had problems with prison guards when they sought access to patients.
She said the situation at the prison was "much worse now" with many more patients following a surge in prisoner numbers, but not enough guards, doctors and nurses.
That made it unsafe for inmates which was "very frustrating and traumatising" for medical staff, the doctor said.
Earlier on Friday, a prison nurse tearfully apologised to the family of Mr Hunt, saying he could have done better caring for him.
The nurse, whose identity was also suppressed, admitted he failed to do medical tests on the new inmate as required under the jail's epilepsy treatment guidelines.
As a nursing team leader at the prison, he said he was overloaded with other work amid staff shortages and was unable to conduct the tests.
He said he was "non-confrontational" and had lacked confidence to ask the guards to stop roughly handling Mr Hunt, who had a prosthetic limb after losing his leg in a motorbike accident in 2008.
The nurse on Friday became tearful as he apologised to Mr Hunt's family, including his wife Rhonda Phillips, who were sitting in the public gallery.
"I'm really sorry for this incident ... I extend my condolences to the whole family. I could have done better in advocating for Mr Hunt," the nurse said.
Mr Hunt was only days into a sentence for dangerous driving causing death after he accidentally hit his ute's accelerator and fatally crushed an 11-year-old boy against a wall at a supermarket in 2022.