Being anywhere near train tracks, at any time, was "stupid and dangerous", rail services manager Craig Inger said.
"It's also costly, with ratepayers and taxpayers forking out tens of thousands of dollars a year to cover up the damage.
"Improved security at railway stabling yards has seen the problem move onto suburban rail lines in recent years. The region's new fleet of electric trains are also faster and quieter than the old diesel units and this poses an even greater risk."
The graffiti incident took place at the same time as a man was trespassing on the tracks at Orakei, Auckland Transport said.
A search was launched after it appeared a man was hit by a train at Orakei and then fled the scene. Trains on the eastern line were suspended as police searched for the man.
A train driver had reported the incident at around 6.30pm, police said last night, and police dogs and a helicopter were sent out to scour the area. However, the man could not be found.
The man had jumped a fence and ran across the tracks in front of the train before he was hit, Inspector Tony Wakelin of the police northern communications centre said last night.
"This was a dangerous and foolish act and the young man is very lucky not to have been killed."
Today, police said the man who had been clipped by the train had not yet been located or identified.
The graffiti incident had also been reported to police, with CCTV footage given to investigating officers.
The footage was being assessed to "determine what, if any, leads it may identify for follow-up inquiries", a police spokeswoman said.
Auckland Transport was hit with a third incident last night, as a signal fault at Britomart station caused delays and cancellations through peak evening traffic. Trains were running at a 30 minute frequency, with all buses accepting train passengers with train tickets.
The disruptions continued this morning, as a signal fault at Ellerslie caused delays on the southern and Onehunga lines. Auckland Transport apologised "for any inconvenience caused".
