The Veterans Affairs Department quietly moved this month to ban flying of Confederate flags from fixed flagpoles at the cemeteries it runs, striking yet another blow against the controversial emblem.

Congress had debated and rejected that change, but the Obama administration decided to move forward anyway, saying it was unilaterally imposing the restrictions.

“In particular, we will amend our policy to make clear that Confederal flags will not be displayed from any permanently fixed flagpole in a national cemetery at any time,” wrote Ronald E. Walters, under secretary for memorial affairs at the VA.

PHOTOS: Best concealed carry handguns

Rep. Jared Huffman, a California Democrat who had pushed for the changes, declared victory after the move, and said it was a rejection of some of the sentiments seen at rallies for GOP presidential hopeful Donald Trump.

“While racist individuals and groups continue to embrace the Confederate battle flag, it has never been more clear that this anachronistic symbol of hatred, slavery, and insurrection should not be promoted or gratuitously displayed on federal property,” Mr. Huffman said in releasing the VA letter last week.

The new policy’s reach is rather slim substantively — currently, Confederate flags were allowed to be flown from VA cemetery flagpoles on Memorial Day and Confederate Memorial Day. But it is the latest in a long-running symbolic battle against the flag.

PHOTOS: 13 Things Liberals Want To Ban

The fight began anew last year after a white man went on a killing spree at a black church in Charleston, South Carolina, slaying nine parishioners. Dylann Roof, whom prosecutors are seeking the death penalty for, posted photos of himself holding a Confederate flag, and wrote white supremacist tracts, prosecutors say.

His use of the flag became a flash point, and South Carolina quickly retired the Confederate flag from an honored spot at a memorial on the state Capitol’s grounds. The push to remove the flag from elsewhere in public life has raged since, with some lawmakers trying to oust from the U.S. Capitol any state flags that pay homage to the Confederacy.

The VA was the last federal department that allowed Confederate flags to be flown from flagpoles. Now the department is in line with the National Park Service and the Army, both of which also maintain cemeteries and which allow groups to place Confederate flags at individual grave sites on Memorial Day and Confederate Memorial Day, but the flags must be removed after the observance.

Mr. Huffman has won House floor votes in both 2015 and 2016 on amendments that would have prohibited flying the Confederate flag from VA flagpoles. Last year, the fight snagged the entire spending process, while this year GOP leaders quietly deleted the confederate flag language from a final House-Senate compromise.

Mr. Walters, in his letter to Mr. Huffman, said the National Cemetery Administration had been awaiting direction from Congress but this summer decided it was moving ahead anyway.

“Although it appears that Congress will not adopt any modifications … NCA has decided to reverse its policy in a manner that is consistent with the House amendment,” he wrote.