"The executive order calls for refugees that were ready to travel where it could cause undue hardship, that they should be considered for waivers. We have done that, in concert with our Department of State colleagues -- 872 refugees will be arriving this week and we'll be processing them for waivers through the end of the week. And that's fully coordinated," said Acting Customs and Border Protection (CBP) Commissioner Kevin McAleenan during a press conference.
There was widespread confusion over the weekend at airports around the world after Trump signed the executive order last Friday. The directive prohibits citizens from seven Muslim-majority nations (Iraq, Iran, Libya, Somalia, Sudan, Syria and Yemen) from entering the U.S. for 90 days. It also temporarily suspends admission for refugees for 120 days and indefinitely bars refugees from Syria.
The order sparked protests across the country -- at airports and in front of the White House -- as well as legal action, which in some cases prompted changes to CBP's procedures.
CBP, along with Immigration and Customs Enforcement (ICE), are overseen by DHS.
Kelly pushed back on criticism of Trump's order, saying that it is "not a travel ban" but a temporary pause that allows DHS staffers to review the existing refugee and visa vetting system.
He said DHS will analyze and assess the "strengths and the weaknesses of our current immigration system, which is the most generous in the world" over the next 30 days. The department will then provide foreign partners with 60 days to cooperate with our national security requirements, he explained.
The secretary said the security analysis "is long overdue," and the department's career intelligence officials supported it.
Kelly denied that the ban targeted Muslims and promised to implement the president's executive orders “professionally, humanely and in accordance with the law.”
"I will not gamble with American lives,” he said.
Within the first 72 hours of the order, the U.S denied boarding to 721 travelers that had visas from the affected countries, according to CBP. In addition, CBP said it processed waivers for 1,060 lawful permanent residents of the United States, and granted an additional 75 waivers to immigrant visa and non-immigrant visa holders.
McAleenan said that lawful permanent residents and special immigrant visa holders are allowed to board their flights and will be processed for a waiver upon arrival.
He also clarified questions about whether dual-nationals are treated differently because of the order. Travelers will be assessed at the U.S. border based on the passport they present, he said.
"If you're a citizen of the United Kingdom, you present your United Kingdom passport and the executive order does not apply to you upon arrival," McAleenan said.
Members of Congress and attorneys general across the country sharply criticized the order on both substance and execution.
When pressed on whether the DHS was fully informed of the executive order in advance of Friday's signing, Kelly told ABC News' Senior Justice Correspondent Pierre Thomas that he knew Trump was going to sign an order a "year-and-a-half or two years before he became the president-elect."
As early as November 2015 on the campaign trail, Trump talked about his concerns over refugees entering the U.S.
"We have no idea who these people are. When the Syrian refugees are going to start pouring into this country, we don’t know if they’re ISIS, we don’t know if it’s a Trojan horse. And I definitely want a database and other checks and balances. We want to go with watchlists. We want to go with databases," Trump told ABC News' "This Week" then.
On Monday night, former Acting U.S. Attorney General Sally Yates issued a letter to Department of Justice staff directing them not to defend the president's order, writing that she was not convinced it is "lawful."
She was fired Monday night and quickly replaced by Dana Boente, the former U.S. attorney for the Eastern District of Virginia.
In a statement, the White House said Yates "betrayed the Department of Justice" and was "weak on borders."
Boente has since rescinded the guidance in Yates' letter and directed staffers "to do our sworn duty and to defend the lawful orders of our president."
When asked about people with special immigrant visas who were denied boarding their flights, McAleenan said that "there were carriers that over-interpreted our guidance."
"We've taken steps contacting a relative in the U.S. to find someone who was already denied boarding foreign so they -- we can tell them that they'll be allowed to board. We've worked very hard to correct and clarify any of those issues," he said.
McAleenan said CBP has now communicated with the State Department and government employees are working with airlines to make sure the rules are implemented correctly.
"It's fair to acknowledge that communications, publicly and interagency, haven't been the best in the initial roll-out of this process," said McAleenan.
Editor’s note: This story was updated after publication to note that it was Acting Commissioner Kevin McAleenan, and not DHS Secretary John Kelly himself, who announced that 872 refugees will be admitted into the U.S.