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LEXINGTON, Ky.—A chemical weapons storage site in Kentucky will be the nation’s lone stockpile to miss a 2017 deadline imposed by Congress for destroying the deadly munitions, the Pentagon said Thursday.

Although Blue Grass Army Depot in Richmond holds just 2 percent of the World War II-era rockets set to be eliminated under an international treaty, it will be the last to start the process and the last to finish, according to a report sent to Congress.

Under the estimate, Blue Grass will begin destroying its weapons in 2019 and finish in 2021. Another storage site in Pueblo, Colo., that also plans to use chemical neutralization rather than incineration will begin in 2014 and end in 2017.

Jean Reed, the Pentagon’s deputy assistant for biological defense and chemical demilitarization, said it is impossible for either site to achieve a 2012 destruction deadline mandated under the international treaty. However, 90 percent of the American stockpile will be destroyed by then, using incinerators at other sites, he said.

A spokesman for Senate Minority Leader Mitch McConnell, a Kentucky Republican, said the current projections are still better than previous estimates and there is still a chance the Pentagon will comply. McConnell has included extra money in congressional spending bills for the project in recent years to speed the clean up.

The destruction date in Colorado and Kentucky has been a moving target for years.

Reed said he was confident this one will stick but made no promises.

“Those have a reasonable confidence level … but don’t buy any lottery tickets on them,” Reed said.

Reed said delays were partly due to increased construction costs and the redesign of a building at the Blue Grass Army Depot that will be used in the destruction of the munitions.

The new finish date is actually two years earlier for Blue Grass and three years earlier for Pueblo than a projection made last fall. That is because President Barack Obama’s budget request calls for a major funding boost for the program—including $250 million more in 2010.

Reed said additional money beyond that wouldn’t be able to further speed up the timeframe, but less could slow it down.

While the Pueblo stockpile is larger than the one in Richmond, it only houses mustard agent. Blue Grass is more complicated because it also holds VX and GB.

When one steel container holding liquid sarin leaked at Blue Grass, an emergency operation was conducted to destroy it and two others ahead of schedule. Reed said that operation had no bearing on the timetable for destroying the larger stockpile.

Carmen Spencer, deputy assistant of the Army for elimination of chemical weapons, said the mustard rockets in Kentucky will be last to go under the program.

“It is the priority of the department to destroy nerve agent projectiles first because they represent the greatest potential risk to the public,” he said.

The Pentagon also said that hydrolysate, a byproduct of neutralizing the agents, would continue to be destroyed at the Kentucky and Colorado sites instead of being shipped to other locations. Local officials had lobbied for the on-site destruction because moving the agent could have posed other risks to local communities.

Congress last year imposed its 2017 deadline for destroying all weapons after a request from McConnell.

Craig Williams of the watchdog group Chemical Weapons Working Group said he had been holding the Pentagon to that date.

Although he acknowledged disappointment that deadline now will be missed for Kentucky, he said he was hopeful the new schedule is achievable.

“What we’ve got today is finally a definitive projection of what we’re looking at,” Williams said.

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