"Our thoughts are with the family during this difficult time, and we will continue to support them in any way we can.
"Our students, staff and the wider school community have been informed of the incident. Support from the school counselling team and the Ministry of Education's Emergency Team is in place for those who may need assistance."
He says the school community will be updated on the situation, where and when appropriate and the school was assisting authorities in their investigations.
The main rail line from Hastings to Napier crosses Ellison St, which at that time of day is also a busy street for work commuters and school traffic.
The lengthy southbound train had stopped across the crossing, extending from the engine about 200 metres to south of Ellison St to the rear just a few metres on the city side.
It happened less than a kilometre from Napier Boys' High.
A cyclist has been injured after reportedly being struck by a train in Napier. Photo / NZME
Napier Mayor Kirsten Wise said, "Our thoughts go out to the young man involved in this collision, his family and his friends. I also acknowledge the efforts of those first on the scene.
"As further details are made available, Napier City Council will work with KiwiRail and Waka Kotahi NZ Transport Agency to fully review this incident."
A St John Ambulance Service spokesman said soon after the incident an ambulance had taken one person from the scene to Hawke's Bay Hospital in Hastings in a critical condition where he remained in a critical condition as of 5pm.
About 4km of the Marine Pde and SH51 stretch from Warren St to Awatoto Rd was also closed as emergency services amassed at the scene, with traffic being diverted on McGrath St and Te Awa Ave.
Police said late Thursday morning the crossing and therefore the Ellison St entrance and exit on the beachfront road would be closed most of the day.
KiwiRail chief operating officer Todd Moyle said their thoughts were with the friends and family of the cyclist.
"Incidents like this are extremely upsetting for all those involved, and our thoughts are with the family and friends of the cyclist," Moyle said.
"In line with our standard practice our driver and all of our staff involved will be offered support from KiwiRail.
"The train was a freight service travelling from Napier to Hastings."
This week is KiwiRail and Tracksafe NZ's annual Rail Safety Week, with a particular focus on crossings in rural areas and provincial centres.
Hawke's Bay has in recent times had one of the lowest rail accident rates in the country, but there is a high incident rate on the highway in the road network around the intersection.
Government last year dedicated $2.75 million to improvements relating to access across the highway and the crossing, the intersection also being next to the entrance to a freedom camping carpark and a bicycle pump track.
One crash between a train and a light motor vehicle occurred in the year ended June, but there have been other crashes and tragedies on the road, and 3km south of the crossing an intersection has seen five fatalities in the past three years.
Waka Kotahi NZTA and the Napier City Council are understood to have had some discussions relating to improvements because of the growing traffic numbers and diverse nature of the crossing, the intersection and other nearby aspects.
A spokesperson for Waka Kotahi NZTA said they were unable to provide comment while police were investigating.
In the past three years, it had completed more than 30 level crossing upgrades around the country, including the SH51 Ellison St.
This included better signage and the installation of barrier arms, flashing lights and bells, which are all aimed at making people's journeys safer.
"Generally for SH51, we are undertaking a review of speed limits and expect to be able to provide an update on this in the coming months."
