Two girls were waiting for a relative to finish work at a Nebraska biofuel plant when all three were killed in a massive explosion that shook the town, officials say.

Fremont Mayor Joey Spellerberg said at a news conference that the children were at the Horizon Biofuels plant ahead of a doctor’s appointment, and although he wasn’t sure of their exact ages, he believed both were under age 12. Dodge County Sheriff Sergeant Brie Frank later confirmed the three were family.

The wreckage still smouldered and the building's large concrete structure remained unstable more than a day later, Frank said, but heavy equipment was brought in to remove rubble, and allow crews to suppress the fire and access part of the building.

The plant makes animal bedding and wood pellets for heating and smoking food, using tons of wood waste. Spellerberg said authorities believe the blast was likely a wood dust explosion in the tall elevator tower.

“That’s really the only thing that makes sense,” Spellerberg said. He said Horizon Biofuels is cooperating “as far as I know”.

'My heart hearts' - Fremont Mayor Joey Spellerberg. - KETV via AP

The company did not immediately respond to phone calls seeking comment.

The top of the elevator tower was torn apart, exposing a mangled concrete-and-rebar core. Metal siding on the building below was left crumpled and charred, while wisps of white smoke drifted into the air Wednesday despite rain overnight.

Spellerberg said fire crews were evaluating whether the whole facility might collapse, making it difficult to get inside as they battle the fire.

“It’s going to be very slow,” said Carl Nielsen of the city’s volunteer fire department. Frank said there is not a timeline for when they expect to bring the two other bodies out.

“My heart hurts,” Spellerberg said. “It’s a tragedy. We pray for all the families involved.”

The company has 10 employees, according to the Nebraska Manufacturing Extension Partnership.

A 2014 fire at the building had damaged the electrical system but left the structure intact, according to reporting by the Fremont Tribune. Significant accumulations of wood dust particles can be a fire and explosion hazard, according to the Occupational Safety and Health Administration.

The aftermath of he plant explosion explosion in Fremont, Nebraska. - Justin Bignell via Reuters

Taylor Kirklin, who lives about a half mile (0.8 km) from the building, said her whole house shook from the explosion at around noon, which was so loud she thought someone crashed a car into her family’s dog kennel business on the property.

“We were really unsure when the explosion happened which plant it was, because there are so many in that area,” she said.

Emily Anderson, who lives just blocks from the plant, said she heard “one really big boom” before police cars flooded in.

“There were just huge plumes of very, very black smoke,” Anderson said. “It was scary.”

Fremont, a city of about 27,000 and the sixth-largest in Nebraska, is 32 miles (52 kilometers) northwest of Omaha.