Assistant Commissioner Bob Hill described the attack as abhorrent and said detectives had been deployed across the state in an effort to apprehend the duo.

He said the pair have previously lived in Western Australia, the La Trobe Valley and Melbourne.

"We know who they are," he said.

Authorised officers from Metro Trains had asked the pair, who police believe were "drunk or drug affected", to get off the Glen Waverley line service after boarding at Flinders Street Station and causing issues on the train.

Shortly after getting off at Heyington station, the pair allegedly attacked Mr O'Neill before fleeing.

Health Minister Jenny Mikakos labelled the attackers "idiots" and urged them to hand themselves in.

"It is absolutely appalling that we’ve had someone who was just going about their day in an unprovoked attack, attacked and assaulted and injured," Ms Mikakos said on Monday morning.

"My thoughts are with Chris O’Neill and his family as as he’s recovering from this senseless attack.

"My message to those people who’ve committed this senseless attack on Chris O’Neill is you are idiots, you will be caught and I would encourage you to hand yourself in now."

Assistant Commissioner Bob Hill told 3AW radio that the pair had been acting "in a way that certainly caused concerns for others on the train".

"They were vomiting and urinating in the carriage. Someone on the train alerted the authorised officers ... and they were escorted off the train.

"When they left the train they went to a gate that adjoins or leads into St Kevin's College and they were walking through the college and by chance ran into Chris O'Neill who was also there off-duty," he said.

Mr O'Neill did not disclose to the two men that he was a member of Victoria Police, Mr Hill said, meaning the offenders would likely be charged with serious assault offences, not assault of a police officer.

"I don't want to go into details, but the meeting between Chris and the two young males was by chance. He was there off-duty walking through the college grounds," said Mr Hill.

"There was some sort of interaction between the two, he or may or may not have asked them to leave ... and then they have retaliated with the assault."

Mr O'Neill, who has been in charge of Protective Service Officers and transit police for a number of years, was rushed to the Epworth hospital and is being treated for head injuries and is also believed to have two fractured ribs.

Mr Hill said police will investigate why the two men were not arrested when they were kicked off the train at Heyington.

Detectives have released images of the two alleged attackers and say they have identified them both but are yet to find them.

They are aged 18 and 19, and are known to police.

"We know who they are and we have spoken to their family and associates and I understand they are actively avoiding apprehension at this point in time. My advice is they need to present themselves to the nearest police station sooner rather than later," said Mr Hill.

Police are urging both men to hand themselves in.

Anyone with information or who witnessed the incident is urged to contact Crime Stoppers on 1800 333 000 or submit a confidential report online at www.crimestoppersvic.com.au.

With Yan Zhang and Matilda Boseley