Ray Kelly said heavy rains caused a tree to fall on the tracks, causing the five-car train to derail.
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At least nine people were injured when the first passenger auto overturned and landed in Alameda Creek.
Mr Kelly has said it was “a miracle” no one was killed in the accident.
One waiting family member said he was told that the train derailed between the first and second tunnel through Niles Canyon as the train headed east.
The front vehicle tumbled into Alameda Creek, coming to rest half-submerged.
Along with the one that fell on its side – into the Alameda Creek – the other wound up on land and stayed upright, according to ACE officials cited by CBS San Francisco station KPIX-TV.
Rescue crews battled the creek’s currents to pull passengers from the partially submerged rail auto.
A mudslide most likely swept the tree onto the Altamont Corridor Express (ACE) train tracks Monday evening, Union Pacific spokesman Francisco J. Castillo said. The uninjured passengers were transferred to the Alameda County Fairgrounds by bus.
Earlier in the night, officials reported that 14 people had been wounded, but later clarified that a few with minor injuries had been treated at the scene and were feeling better. At the time of derailment, the train was between Fremont and Pleasanton.
The Fremont Police Department said Niles Canyon Road in Sunol, near the site of the crash, was closed as several agencies investigated the incident.
Around 8:40 p.m., Alameda County Fire Department officials tweeted that all passengers were removed and are being assessed.
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“ACE Train’s No. 1 priority is passenger safety”, Walker said.
