The world's second-largest plane-maker also said it would delay the first flight of the jumbo 747-8 Freighter to 2010 from the fourth quarter of 2009.
Boeing said $640 million of the charge reflects higher estimated costs to produce the 747-8. The company said late maturity of engineering designs disrupted manufacturing in the third quarter.
The remaining $360 million of the charge is linked to tough market conditions and the company's decision to maintain the 747-8 production rate at 1.5 airplanes per month nearly two years longer than previously planned.
Boeing said it now expects first flight of the 747-8 Freighter by early next year with the flight test program taking place in 2010.
First delivery of the 747-8 Freighter is now expected in the fourth quarter of 2010. First delivery of the 747 Intercontinental passenger version remains scheduled for the fourth quarter of 2011.
Boeing said it would update its 2009 financial outlook on October 21 when it reports third-quarter results.
(Reporting by Kyle Peterson, editing by Dave Zimmerman)