The incident occurred on Wednesday at Didion Milling Plant in Cambria. Sixteen people were inside the plant at the time.
The company's corn products are used in brewing beer as well as in making chips and breakfast cereals.
The blast killed Duelle Block, 27, a mill operator; Robert Goodenow, 53, a forklift operator; and Pawel Tordoff, 21, a packing machine operator, according to Associated Press.
"The loss of these three team members is a very emotional time for us and has torn a hole in the heart of the Didion Milling team and the Cambria community," said Derrick Clark, plant executive, Didion Milling Plant.
The cause of the explosion is still under investigation.
US Occupational Safety and Health Administration confirmed the plant was cited in 2011 for not taking precautions against dust explosions.
Dust explosions occur when high concentrations of dust particles are suspended in the air in a confined space during grain handling.
The federal safety agency ordered the mill to correct the problem by April 2011, and records show Didion paid a $3,465 fine and the case was closed in September 2013.
James Brunker, senior executive, M3 Insurance, which insures the company, said the plant's insurance risk assessment has been improving since the violation.
"It's too early for us to comment on any potential sources. We're confidant about the systems we have in place protect our workers," added Clark.
Didion Milling employs more than 200 people at multiple facilities around southern Wisconsin.
The company has closed until further notice, but Clark said all the plant workers will keep their jobs. Some may be moved to other facilities or retrained to handle other duties.
He expects production to resume at an ethanol plant adjacent to the corn mill soon.
Brothers John and Dow Didion began Didion Milling in 1972. Construction on the Cambria corn mill was completed in 1991, according to the website. The company's corn products are used in brewing beer as well as in making chips, breakfast cereals, bathroom moldings, steel and ethanol.