In an interview from Ottawa, Mahboob Khawaja said his son Momin Khawaja complained last year that one of the so-called Toronto 18 terrorists had been threatening him.
As a result of the complaints, Momin Khawaja was moved to a different area of the Quebec prison for more than a month before being returned to the range where he was attacked.
"Momin feared for his life," Mahboob Khawaja told The Canadian Press.
"The authorities should have taken care of this last year when Momin complained."
Momin Khawaja, an Ottawa software developer, was convicted of five terrorism charges in 2008 and, after an appeal, sentenced to life without parole for 10 years.
Along with a handful of other convicted terrorists, including several Toronto 18 plotters, Khawaja has been housed in a maximum security facility in Sainte-Anne-des-Plaines near Montreal.
Khawaja's father, who visited his son on the weekend, said his son suffered burns to almost two-thirds of his body when he was attacked out of the blue on Jan. 16 in a communal area of the range.
The assailant threw a pot with boiling water "mixed with something" on the victim, said Mahboob Khawaja.
He said his son told him Zakaria Amara was the assailant. But authorities would not identify those involved in the incident and Amara's lawyers also could not confirm any details.
Amara, a Toronto 18 ringleader, was jailed for life in 2010 for plotting mass carnage by truck-bombing RCMP headquarters, the Toronto Stock Exchange and other targets.
Khawaja received several hours of emergency medical treatment in hospital in Montreal before being returned to the prison, which only has basic nursing care.
"He was still in a great deal of pain and anguish," Khawaja said of his son, whose appeal is pending before the Supreme Court of Canada.
"My impression was he should have been kept in hospital for medical care and treatment."
He described his son as "worried, down and demoralized."
Correctional Service Canada confirmed it was investigating an incident but would not identify those involved or provide any other details.
Spokesman Serge Abergel, who said charges could flow from the probe, also said he was unaware of past problems involving Khawaja or Amara.
However, he said the service would examine the "incident of violence," as it does in all such incidents, with a view to reducing the chances of further problems.
Both Amara's trial lawyer Michael Lacy and his Appeal Court lawyer James Lockyer said they had no information and could not comment.
Ottawa lawyer Lawrence Greenspon, who represents Khawaja, said he was looking forward to what prison authorities find out.
He also said he wanted to know what they planned to do to prevent a recurrence short of keeping his client in segregation.
Greenspon also said he was unable to explain the reasons for the conflict.
"For some reason, (authorities) have it in their heads that he should be on the same wing or same pod as some of these fellows from the Toronto 18," Greenspon said.
"He had and has no interest whatsoever in being in the same range or pod as any of them."
Abergel said inmates are housed in the most appropriate place, taking into account security concerns and their needs.
Khawaja's father also said he hoped the investigation yields answers.
"We are very worried," he said. "We hope authorities will take appropriate measures to ensure his safety."
He also wondered whether his son could be moved to another maximum security facility where family visits might be easier and they would not have to talk to their son through a screen.