Rail workers have suggested fights between rival groups began as early as 10pm, when ballast rocks were thrown from the rail tracks into carriages.
One source claimed the violence left "pools of blood" around Britomart station.
Trouble also erupted at several other stations including in West Auckland and at Glen Innes, where a citybound train was ambushed about 12.30am on Sunday by hooligans who threw rocks at it, breaking nine windows.
The Rail and Maritime Transport Union, has flagged concerns about the safety of its members and the public but praised a train manager for ordering a train evacuation and moving passengers to a safe point.
"Under no circumstances should rail staff or passengers have to face such security risks in their workplace -- it raises serious questions about the preparedness of security and police to deal with these risks after major events," said union general secretary Wayne Butson.
His members had also raised concern that those involved in the Britomart violence were put into different trains to separate them.
"Putting potentially violent individuals and groups on to the trains puts both staff and passengers at risk."
He also criticised Auckland Transport for allegedly making a resumption of rail services its priority, rather than the safety of staff and passengers, a claim denied last night by the council organisation.
Auckland Transport spokesman Mark Hannan said a decision was made to run the trains out of Britomart on the recommendation of police, to help disperse the crowd, and officers rode on them to control the trouble-makers.
Mr Gibson said police patrolled the rail network in the lead-up to the disorder.
Although they were not at Britomart when it erupted, they detected it from video feed to Auckland Transport's operations centre, and the first of about 25 officers arrived within five minutes.