"Neither the track nor the train was damaged and the line was cleared at 3pm ... the incident is being investigated."
The level crossing had working bells, KiwiRail confirmed. Remarkably, no one was seriously injured in the crash.
A St John Ambulance spokesperson said two people were treated for minor injuries and another person was treated for moderate injuries by paramedics at the scene.
Central Hawke's Bay Police Sergeant Neil Baker said thankfully all occupants involved managed to walk away.
"The circumstances of the crash are still currently under investigation and the intersection will remain closed for the majority of the afternoon while the train and tracks are inspected."
The freight train came to a stop between the Tucker Box shop and the Central Hawke's Bay Museum along High St.
The crash caused significant traffic blockages all through Waipawa until the tracks were cleared.
Baker urged motorists to take extra care on the region's roads as police often saw an increase in traffic during the holiday period.
Forty minutes after the train crash, a truck struck a pedestrian on Taihape Rd, northwest of Hastings.
A St John spokesperson said an ambulance transported one patient with moderate injuries to Hawke's Bay Hospital following the incident.
Meanwhile, another person was seriously injured in another crash on Maadi Rd in Onekawa shortly before 2pm and also taken to Hawke's Bay Hospital, the spokesperson said.
Rain had fallen prior to the crashes. Eastern District Police road policing manager Inspector Matt Broderick said roads were always slippery and hazardous after it rained.
He said particularly following a dry spell, any built-up oil or rubber fragments on the road were flushed out and rose to the surface.
"The first hour or so after it rains is the worst time when it is the slippiest it is going to get.
"That is the time when people need to be super aware and drive to the conditions - it is going to be slippier than perhaps it would be after it has rained for several hours and washed it away."
Broderick reminded motorists to keep their distance between vehicles and drive to the conditions.
"It is a two-second rule normally but it is at least four seconds when it is raining."
He said it is much harder to stop if you needed to brake suddenly.