Ten of them died.
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The Humane Society of Hobart was called to the scene and shot video.
Police said the driver, who picked the dogs up from a flight at O'Hare airport and was bound for a training facility in Michigan City, was unaware that the air conditioning in the cargo area of the truck had failed in the sweltering heat.
Humane society officials said when they arrived to help, they were turned away.
"We had cooling vans and animal care and control vehicles ready to transport, and, because we were asking for that paperwork, it seemed to make the owner mad, and he said he would not allow us to help," said Jenny Webber, with the Hobart Humane Society.
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Lake Station police would not comment, but posted a narrative of the situation on Facebook, calling it a freak event and not a matter of neglect on the part of the truck's driver.
They went on to write the scene was chaotic, and took an emotional toll on all that were involved in trying to save as many canines as possible.
The humane society said they believe the dogs were en route to a Michigan trainer to become police dogs.
"This is truly a sad day for all of us," Webber said.
Five of the German shepherds being transported remain hospitalized. The humane society is taking custody of them, and said the owner is welcome to come pick them up if he can show the proper paperwork.