A fire that began in a rubbish pile at a construction site on the upper level of the Queensboro Bridge yesterday quickly spread to scaffolding and engulfed the tarpaulin that encased the bridge’s steel columns and trusses, shutting the bridge for hours, fire officials said.

The fire was reported at 12:53 p.m., and it took nearly two hours and more than 100 firefighters to bring the three alarm blaze under control. Five firefighters reportedly suffered minor injuries.

After initially closing both levels of the bridge, transportation officials reopened the lower level during the height of rush hour after engineers assessed the structural damage caused by the fire. The upper level is expected to reopen by this morning after transportation crews repave and paint part of the roadway.

Fire officials said they are investigating the cause of the fire, which they said originated on a work site of L & L Painting Company Incorporated, which has a $167 million, five-year contract to strip the bridge of its lead paint and repaint it.

The Hicksville, N.Y., company, which also has a $54 million contract with the Port Authority of New York and New Jersey to paint the George Washington Bridge as well as a contract to paint the Williamsburg Bridge, did not respond to requests for comment yesterday.

The company was the source of several complaints last year from motorists, who told transportation officials that errant sand-blasting pellets cracked their windshields, a spokesman for the Department of Transportation, Craig Chin, confirmed. He said only one of the incidents was substantiated.

Earlier this year, the company settled a $15,000 workers’ compensation claim by a painter who was injured while working on the Williamsburg Bridge.

During a 24-hour period measured in 2003, the last date for which statistics are available, transportation officials counted 92,851 cars driving across the Queensboro Bridge into Manhattan at 59th Street, and 92,113 cars traveling toward Queens.