The uproar in the
Southern Republicans protested the Californian's move and threatened to pull their support for the broader $30-billion bill, which funds the Interior Department and other related federal agencies, including the national parks.
But the compromise backfired and was seen as too weak by Democrats, who accused the GOP of protecting what many view as a racist Southern symbol of slavery.
The battle over the flag was heightened by the racially-motivated shootings last month in Charleston, S.C.
"When you hear me say that congressional Republicans have an agenda that is out of step with the vast majority of Americans, this record at least in part is what I'm referring to," said White House Press Secretary Josh Earnest.
Earnest criticized House Republicans as having "values and priorities that lie elsewhere."
The debate is one that Republicans in Congress had been hoping to avoid as the party continues to reel from perceptions that it is not inclusive or tolerant of minority groups, especially in the aftermath of presidential candidate Donald Trump's disparaging remarks about Mexican immigrants.
But the uproar, coming late Wednesday just as the South Carolina legislature was taking steps to remove its Confederate flag from the Capitol grounds, proved an easy target for Democrats to attack the GOP as out of touch.
Boehner and McCarthy had no choice but to halt further proceedings on the legislation Thursday. The speaker called for an informal bipartisan task force to develop a compromise.
"I actually think it's time for some adults here in Congress to actually sit down and have a conversation about how to address this issue," Boehner said Thursday.
Boehner lamented that the issue had become a "political football," and promised talks in "coming days."
Rather than ban the flag outright from national parks and gift shops, as Huffman's amendment proposed, the GOP compromise from Calvert would have mirrored directives from the White House that limit the Confederate flag's display at national parks largely to the Confederate Memorial Day. The administration directive also gives park superintendents authority to remove Confederate items from gift stores.
Democrats, though, preferred tougher language, as proposed by Huffman.