Attorney General Loretta Lynch overruled FBI Director James B. Comey this week, saying the Obama administration does support denying firearms sales to those on terrorist watch lists and that it can be done without harming investigations.

Mr. Comey last year had told Congress that denying sales could “blow” his agents’ investigations into potential terrorists. But his superiors at the Justice Department issued a statement Thursday saying they want to see Congress approve the “no-fly, no-buy” plan Democrats are pursuing.

“The amendment gives the Justice Department an important additional tool to prevent the sale of guns to suspected terrorists by licensed firearms dealers while ensuring protection of the department’s operational and investigative sensitivities,” department spokesman Dena Iverson said in a statement.

In the wake of the weekend’s terror-related shooting at a gay nightclub in Orlando, Democrats have zeroed in on guns, arguing that Omar Mateen’s rampage could have been avoided had Congress enacted a ban on gun sales to those on the government’s watch lists, which are supposed to detail those known or suspected to have ties to terrorism.

The FBI has poked holes in that theory, saying that while Mateen had been listed while under investigation a few years ago, he had been removed after the agency was unable to make a case against him.

Under the current system, if someone on the list attempts to buy a firearm, the sale isn’t automatically stopped — but agents are alerted and use that information to help their investigation.

Mr. Comey testified to Congress last year that if a sale is stopped altogether, it could tip off someone to the FBI’s investigation.

“It’s a little bit challenging for us because ‘known’ or ‘suspected’ means it hasn’t been adjudicated in every case that somebody is a terrorist,” Mr. Comey told Sen. Dianne Feinstein, chief sponsor of the watch-list gun control proposal. “It’s somebody we’re investigating, so we don’t want to, obviously, blow our investigation.”

House Speaker Paul D. Ryan said Mr. Comey reiterated those concerns in briefings to lawmakers this week.

“If we do this wrong, like the president is proposing, we can actually blow our ongoing terrorist investigations. So, we want to get this right, so that we don’t undermine terrorist investigations,” Mr. Ryan said.

Democrats have brushed aside those concerns, and conducted a quasi-filibuster on the Senate floor Wednesday to insist on holding a vote on their proposal to outright ban sales.

Republicans argue that the lists are shrouded in mystery, including how someone is listed, and they predicted an outright ban would be ruled unconstitutional because it denies Second Amendment rights without the due process of a judge’s review.

Sen. John Cornyn, Texas Republican, has countered with a proposal that would send an alert if someone on the terrorist watch list, or who had been on it within the last five years, attempts to buy a firearm or explosive. The sale could be delayed three days while the Justice Department goes to court to make the case that the transfer should be denied.

Mr. Cornyn’s bill would require the person be notified of the proceeding.

Democrats say Mr. Cornyn’s proposal puts too much of the burden on the government, though Mrs. Feinstein’s latest proposal does move closer to the GOP’s stance.

Her amendment would grant the attorney general power to halt a gun sale based on “reasonable suspicion” of terrorist connections, but would allow the purchaser to seek review from a judge. The government could take steps to try to keep proceedings secret if they “could be expected to result in damage to national security or ongoing law enforcement operations.”

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