WASHINGTON — In 1987, the Army estimated it would cost $2 billion to dispose of the 27,768 metric tons of chemical weapons in its stockpile.

Today, the price has mushroomed to $28 billion, and the military is about a third of the way through the job. An array of problems — including technical challenges and protests from community activists concerned about the impact of burning the weapons — have dogged the progress. In May, officials announced the Army will be unable to destroy all the weapons by 2012 — which would be a five-year extension to the current deadline.

"We underestimated the job, the complexity of the job and this high-hazard environment we have to operate in," said Michael Parker, director of the Army's Chemical Materials Agency.

The United States has the second-largest inventory of chemical weapons next to Russia, which has 40,000 tons of warfare agents and is also struggling to meet the 2007 disposal deadline under an international treaty dating to 1997. Both countries are seeking five-year extensions.

The Army is incinerating weapons in Utah, Alabama, Arkansas and Oregon, and has finished work on Johnston Atoll in the Pacific. The Deseret Chemical Depot incinerator in Utah's Tooele County has destroyed more than 54 percent of a weapons stockpile — the nation's largest — stored in nearby earthen igloos.

But under pressure from activists, the Pentagon has abandoned incineration for chemically neutralizing warfare agents in Colorado, Indiana, Kentucky and Maryland. It has completed work in Maryland, but plant construction in Colorado and Kentucky will only begin this year. By Parker's estimate, the chemical neutralization facilities will not finish disposing of warfare agents until 2014.

"We are making progress every day," Parker said. "Some days are better than others."

Congress mandated disposal of the weapons a decade ago, and ever since, the Defense Department has been battling environmental activists and some members of Congress over its reliance on burning the chemicals.

Pentagon officials have argued that incineration is most efficient. But Craig Williams, director of the Chemical Weapons Working Group in Berea, Ky., said that emissions could have lasting effects on communities such as his. Working with Sen. Mitch McConnell, R-Ky., he has spent nearly two decades pushing the Army to develop a chemical neutralization approach.

"We basically ended up forcing them to consider alternative disposal methods," McConnell said. "Environmental cleanup, I guess, is not high in the mission statement" of the Defense Department.