Homeland Security Secretary John F. Kelly pauses while speaking at a news conference in Washington on Jan. 31. (Andrew Harnik/Associated Press)

Editor’s Note: Prior to publication of this column, The Post sought comment from the Department of Homeland Security but not from the White House. We should have done both. The article has been updated. – Fred Hiatt

UPDATE (Feb. 4, 6:13 p.m.): The article has been updated to reflect comments from White House press secretary Sean Spicer. The article previously stated that Stephen K. Bannon visited Homeland Security Secretary John F. Kelly’s office on Jan. 28. Spicer said Bannon did not make such a visit. He also said that Secretary of State Rex Tillerson and Bannon did not participate in a 2 a.m. conference call on Jan. 29. The article also previously stated that President Trump approved a pause in executive orders pending new procedures. According to Spicer, it was White House Chief of Staff Reince Priebus, rather than the president, who approved the new procedures, but not a pause.

UPDATE (Feb. 5, 8:55 a.m.): This post has been updated.

Over the weekend of Jan. 28-29, as airport protests raged over President Trump’s executive order on immigration, the man charged with implementing the order, Homeland Security Secretary John F. Kelly, had a plan. He would issue a waiver for lawful permanent residents, a.k.a. green-card holders, from the seven majority-Muslim countries whose citizens had been banned from entering the United States.

White House chief strategist Stephen K. Bannon wanted to stop Kelly in his tracks and told him not to issue the order. Kelly, according to two administration officials familiar with the confrontation, refused to comply. That was the beginning of a weekend of negotiations among senior Trump administration staffers that led, on Sunday, Jan. 29, to a White House decision to change the process for the issuance of executive orders.

The disagreement between Bannon and Kelly pitted a political operator against a military disciplinarian. Two administration officials gave the following account of their exchange: Respectfully but firmly, the retired general told Bannon that despite his high position in the White House and close relationship with President Trump, the former Breitbart chief was not in Kelly’s chain of command. If the president wanted Kelly to back off from issuing the waiver, Kelly would have to hear it from the president directly, he told Bannon. White House press secretary Sean Spicer said Kelly and Bannon spoke on Jan. 27 and 29, but denied they had a confrontation over the green card waiver. In an email sent late Saturday, Bannon also denied a confrontation with Kelly and said he had not told him to withhold the waiver.

Trump didn’t call Kelly to tell him to hold off. Kelly issued the waiver late Saturday night, although it wasn’t officially announced until the following day.

Here's what you need to know about the man who went from Breitbart News chairman to Donald Trump's campaign CEO before his appointment as chief White House strategist and senior counselor. (Jenny Starrs/The Washington Post)

That did not end the dispute. At approximately 2 a.m. Sunday, according to the two officials, a conference call of several top officials was convened to discuss the ongoing confusion over the executive order and the anger from Cabinet officials over their lack of inclusion in the process in advance.

On the call were White House senior policy adviser Stephen Miller, White House Counsel Donald McGahn, national security adviser Michael Flynn, Kelly, Defense Secretary Jim Mattis and a senior State Department official, who represented the State Department because Secretary of State nominee Rex Tillerson had not yet been confirmed.

One White House official and one administration official told me that the Cabinet officials presented a united front and complained about the process that led to the issuance of the immigration executive order, focusing on their near-complete lack of consultation as well as the White House’s reluctance to make what they saw as common-sense revisions, such as exempting green-card holders.

Bannon and Miller pushed back, defending the White House’s actions and explaining that the process and substance of the order had been kept to a close circle because the Trump administration had not yet installed its own officials in key government roles and other officials were still getting settled into place.

Flynn, according to the White House official, partially sided with the Cabinet officials, arguing that they should be included in the process, even if the White House ultimately decided not to adopt their recommendations.

“Flynn’s argument was a process argument, that we are unnecessarily putting these guys in a tough position,” the White House official said. “If you are going to ignore them, you have to at least give them a chance to say their piece.”

Later on Sunday, White House Chief of Staff Reince Priebus met with senior staff and made a decision at that, following the already scheduled rollout of an executive order on regulatory reforms, all other executive orders would be held up until a process was established that included the input of key officials outside the White House.

Spicer told The Post that there was no pause and that Priebus simply issued new procedures for executive orders that were meant for improving the process.

“We have to evaluate the way we get input from the Cabinet secretaries affected before we do things,” the White House official said. The pause appeared to end on Friday, when Trump signed an executive order and a memorandum on financial regulation.

Retired Marine Gen. John F. Kelly is the secretary of homeland security under President Trump. Here's what you need to know about him. (Sarah Parnass,Osman Malik/The Washington Post)

The weekend’s events were the first major dust-up between the White House political leadership and the powerful figures Trump has appointed to head the national security bureaucracies. The Cabinet members stood up for themselves and their agencies and successfully pushed for a policy tweak that the administration later embraced in a memorandum to “clarify” the executive order.

The Cabinet members also demonstrated that they had something to offer the White House besides their policy input; they are the most credible spokespeople for controversial White House policies in the eyes of the public. On Tuesday, Kelly gave the White House badly needed political cover by holding a news conference and strongly defending the immigration executive order.

“This is not, I repeat, not, a ban on Muslims,” Kelly said. “We cannot gamble with American lives. I will not gamble with American lives. These orders are a matter of national security, and it is my sworn responsibility as secretary of homeland security to protect and defend the American people,” he said.

He said the DHS would implement the order “humanely,” that the DHS lawyers had been involved in preparing the order and that he did have some advance notice, denying reports he found out about it being signed while he was on an airplane. “We knew it was coming. It wasn’t a surprise,” Kelly said.

Minutes later, Spicer told reporters at the daily briefing that “there was proper coordination and preparation” between the White House and the DHS.

If the White House is now serious about working with the Cabinet, that’s a positive sign and means that this series of events had a constructive impact on policymaking. But there’s a good chance that this won’t be the last time that Cabinet secretaries will have to confront Bannon and Miller. Score their first battle as a tie.