The state fire marshal's office was not called in, officials said.
Investigators cautioned the workers from a private contracting company hired by the warehouse owners to clear away some debris but not to disturb areas still under investigation.
A damage estimate was not available. The warehouse, a distribution center for books from a number of publishers, held hard cover and paperbacks on shelves as high as eight tiers off the floor.
A company official said Tuesday night there were millions of dollars worth of books in the facility.
The height of the stacks and the weight of the water-soaked cartons of books threatened to collapse on the firefighters working inside the warehouse Tuesday night, officials said.
Fire crews were expected to remain on the scene through the night Wednesday to douse any hotspots that might rekindle.
Some firefighters like Mike Kriner, who was leaning against the warehouse looking exhausted Wednesday afternoon, had been at the scene since shortly after the alarm went out at 8:37 p.m. Tuesday.
Many went home to get some sleep.
"Stubborn is not the word for this fire," Kriner said.
He was one of the first to go inside the building, he said.
"At first we couldn't tell there was a fire. The lights were still all on," he said. "Then we went toward the back of the building and saw the flames. I said 'yeah, we got a big fire here.'"
A trip through the warehouse Wednesday evening showed where the blaze had done its worst.
Rugged steel girders and shelving lay twisted. Tiers still standing held stacks of soggy book-filled cardboard boxes. Piles of books, charred and soggy, lay in heaps in the aisles.
Water damage was caused by a combination of the water poured into the building by firefighters and by the water from the building's own sprinkler system, one fire official said.
"It's still flaring up," said Troy Wagaman, deputy chief of the Blue Ridge Summit Rescue Squad. The Blue Ridge Summit Fire Department supervised the fire-fighting operations.
The smoke was so heavy, even after the fire was knocked down, that two airboats with their powerful propellers were taken in to clear smoke from inside the building.
Company officials could not be reached for comment Wednesday.
Approximately 500 people work at the University Press of America complex, including about 150 in Encore Marketing, according to Carol Henicle, executive director of the Greater Waynesboro Area Chamber of Commerce, who toured the damaged facility Wednesday with L. Michael Ross, president of the Franklin County Area Development Corp.
Henicle said Encore Marketing, customer service and office personnel were back in their work areas. She said company officials' biggest worry was taking care of their customers and suppliers while the damage is repaired.
"They need to get up and running as soon as possible," she said. "They're coming into their busiest season of the year, the Christmas season."
National Book Network employee Sandy Wetzel said many workers fear there could be layoffs as a fallout from Tuesday's blaze.
"There's always a worry (about job security)," Wetzel said. "Hopefully, things here will get back on track soon."
Wetzel said a message left on the company voicemail instructed employees not to report for work Wednesday.
Kenneth Davis, a book packer, said Wednesday night there had been no word from supervisors on whether warehouse workers were to report to work today.
"I guess I'll call in the morning to find out," he said.
"The earliest I can imagine them having things back in order is the first of next week," Ross said. "The damage in terms of inventory is pretty extensive, probably more lost to water damage than the fire itself."
Jim Barton, an employee of Unique Bar & Grill, a popular hangout for workers at the warehouse, said the mood in the bar Wednesday evening was somber.
"A lot of employees I talked to just bought cars or homes and were concerned about how they were going to make payments," Barton said. "It's a shame."
A sign saying "Building E," the same designation as the warehouse damaged by the fire, hangs over the Unique's bar near the front entrance.
Barton said the sign was put up years ago, before the current Building E warehouse was erected, by employees who adopted the building for unofficial meetings.
Staff writers Don Aines and Brian Shappell contributed to this story.