Washington (CNN) The newly installed secretary of homeland security on Tuesday defended the rollout of the controversial executive order by President Donald Trump over the weekend, saying that he and his agency had been fully involved its drafting.

The news conference by Secretary John Kelly came after days of confusion at US airports and overseas about what was intended by the order, which temporarily bans refugees and individuals from seven countries designated as high risk from entering the US.

"I knew this was under development, and I think we were in pretty good shape on how it was implemented by the workforce," Kelly told reporters who repeatedly asked when he found out about the order and how his agency set about enforcing it.

CNN reported that it wasn't until the day the order was signed that career staff at Homeland Security were able to see the final details. Numerous officials told CNN the traditional inter-agency process had been side-stepped and the White House largely worked on the order in isolation.

How to deal with US green card holders shifted as the order was put in place. At first, DHS interpreted the order to not apply to legal permanent residents and issued that to airlines. The White House overruled that on Friday night, before later clarifying that judgments would be made on a case-by-case basis and legal permanent residents would be allowed in barring other concerns.

Customs and Border Protection Acting Commissioner Kevin McAleenan acknowledged Tuesday that communication broke down, after he faced repeated questions from the press about why airlines were given contradictory guidance, why individuals were detained for hours, and about reports that some individuals were given forms to sign giving up their residency status, as well as why the Department of Defense was not aware as of Monday that Special Immigrant Visa holders were allowed to enter.

"I think it's fair to acknowledge that communications, publicly and inter-agency, haven't been the best in the rollout of this process," McAleenan said, in the only instance in the news conference that implementation could have been better handled.

Kelly said on Tuesday that he had seen "at least two" drafts of the order, and that he was aware the order would be signed Friday as of Thursday night.

"I did know it was under development, had an opportunity to look at at least two, as I recollect, drafts as it got closer to Friday," Kelly said, when asked for specifics on who was involved. "Don't exactly know other than my legal shop representatives were involved, I would imagine some, on the landing team (from the transition), I would imagine some of them, but the point is, it came to the department, it was on a close-hold basis."

Kelly said "only the people that needed it," including himself and agency lawyers, were given access. "It was a back-and-forth process, I did talk to a representative in the White House oh probably earlier in the week about where it was going," he said. "Pretty busy week, I didn't get involved in correcting grammar or reformatting the thing."

After his confirmation hearing, Kelly was briefed on all the immigration executive orders under consideration by the administration and then was given the text a few days before inauguration, a White House source told CNN. Briefings also included senior department heads and staffs, as well as "beachhead" teams from the administration in agencies.

The order was also signed off on by the Office of Legal Counsel and the Homeland Security Council and National Security Council, the source said.

Kelly said anyone who had been following Trump's campaign wouldn't be surprised by the travel ban order, but he remained vague on the extent of the involvement of the interagency process.

"I knew he was going to sign an order about a year and half or two years before he became President-elect," Kelly said. "From Day 1, in terms of the inauguration, finishing touches, I have to put it that way, were being put on the executive order. ... People on my staff were generally involved."

Department officials also gave updated numbers on the impact of the order.

McAleenan said in the first 72 hours, 1 million travelers came to the US by air, including 500,000 foreign nationals. He said 721 individuals were denied boarding, but 1,060 legal permanent residents of the US were processed for waivers to enter the US and an additional 75 waivers were given to visa holders.

That went beyond the 109 that the White House said were affected because they were in transit when the order was signed -- numbers that the department officials said only applied to the first day of the order.

Kelly also pushed back strongly on any characteristic of the order as targeting Muslims.

"This is not -- I repeat -- not a ban on Muslims," Kelly said. "Religious liberty is one of our most treasured values"

He noted that the seven countries in the order were the same designated by Congress and the Obama administration for special attention in the past, saying some are in "various states of collapse." The goal, Kelly said, was to allow the US to better screen travelers for terror risk.

"It is easier to play defense on the 50 yard line than the one yard line," Kelly said. "I will not gamble American lives."