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Officials decided to take the step after consulting with members of a national response team from Houston, who were flown in overnight to offer advice, Lincoln Fire Chief Dave Whitt said. The fuel would be flushed it into a massive hole in the ground.
Fire officials initially said the blaze could continue for 21 days, but on Wednesday, Whitt said that scenario was unacceptable. Nearly 5,000 homes in the city of 40,000 are evacuated, and students in the area are missing their first days of school.
Whitt said firefighters now hope to have the blaze under control within 24 to 48 hours.
The danger officials are trying to head off would be a catastrophic failure of the 29,000-gallon tank caused by a buildup of heat, which would lead to an explosion and massive fireball several hundred yards wide.
Whitt said the blaze held the potential for "great catastrophic results." He said firefighters have been successful in keeping the tanker cool since it caught fire Tuesday afternoon but worried that it was showing signs of melting.
"Quite frankly, we are very lucky," he said during a news conference. "We were really able to put a dent in the progression of the fire."
It was unclear how the tanker caught fire. One worker at the rail yard was injured in the initial fire, which erupted at the Northern Propane Energy yard in Lincoln, about 30 miles northeast of the state capital. Whitt said the worker suffered flash burns but has been released from the hospital.
He said the procedure to drain the rail car of propane, called a "hot tap," will begin later Wednesday. He said the tanker will remain in place as firefighters attach a pipe to it and drain the propane into a hole to be dug by bulldozers.
The Associated Press contributed to this report.