WASHINGTON (Reuters) - The Washington National Cathedral will remove Confederate battle flags from two stained glass windows honoring Confederate Generals Stonewall Jackson and Robert E. Lee, the cathedral said on Wednesday.

Officials at the neo-Gothic Episcopal cathedral, one of the best-known U.S. places of worship, said in a statement the two images of the flag would be replaced by plain glass, with the cost borne by private donors.

The rest of the two windows will be left up for the time being and used as a starting point in discussions about racism, they said.

The Rev. Kelly Brown Douglas, a member of a task force that last week recommended removal of the flags, said the Lee-Jackson windows raised the question of race and the legacy of slavery, "and instead of turning away from that question, the Cathedral has decided to lean into it.”

The task force report said the cathedral should readdress the issue of what to do with the Lee and Jackson windows within two years.

The battle flag used by Confederate forces during the 1861-65 U.S. Civil War has been at the center of controversy since a white supremacist allegedly gunned down nine black worshippers at a South Carolina church in June 2015.

Photos of the white man charged in the shooting showed him posing with the flag on a website that also carried a racist manifesto. The massacre has spurred efforts to remove the flag and other Confederate symbols from public places.

The windows at the cathedral were installed in 1953 to foster reconciliation between sections of the United States that had been riven by the Civil War.

Since 1907, the cathedral has been used for state funerals for three presidents, and a number of presidential prayer services. It has also hosted services for noted diplomats and dignitaries.

(Reporting by Ian Simpson; Editing by Peter Cooney)