The car was pushed hundreds of metres down the track before the train could come to a stop.
Morrinsville Volunteer Fire Brigade chief fire officer Brian Watters said his crew were first on the scene when they received the call at 4.09am.
Watters said there was nothing firefighters could do for the two occupants of the car.
Their bodies had to be cut from the wreckage several hours later.
NZ Transport Agency was in the process of installing barrier arms at the blackspot, where a 90-year-old man was killed in March, 2017, and another elderly man was killed there two years prior.
"They're in the process of changing it all," Watters said. "They're upgrading the lights and signals and putting barrier arms on it."
He said the area around the crossing was currently a 30kmh speed limit while the work was being undertaken.
An NZTA spokeswoman said it and KiwiRail were improving 12 level crossings across the Waikato and Bay of Plenty.
She said there had never been barrier arms at the crossing previously.
KiwiRail chief operations officer Todd Moyle said the level crossing was currently protected by flashing lights and bells, and that the barrier arms were due to be installed in the New Year.
"This is a tragic incident and its effects will be far-reaching," Moyle said.
"Our thoughts are with the friends and family of those who have died, and also our driver, who we are providing with appropriate support, including counselling."
The freight train was travelling from Mt Maunganui to Hamilton when the collision happened on the East Coast Main Trunk Line.
Matamata-Piako mayor Ash Tanner called the crash a tragedy and said the council had flagged the awkward intersection as a problem in the past with NZTA.
"So that makes it probably even worse because it is actually getting worked on as we speak, for that reason, so the timing probably couldn't be worse.
"It's gutting. Our thoughts are with the families involved which is pretty terrible, especially at this time of year."
It's understood the pair killed may have been brother and sister. Family were at the crash scene today, supported by police.
The road was closed with diversions in place on SH26 between Avenue Rd and Kuranui Rd.
Police would not confirm details of the crash except to say they were investigating.