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President Donald Trump defended his controversial executive order restricting travel from seven Muslim-majority nations and indefinitely banning Syrian refugees as "not about religion" amid a second day of protests and uncertainty around the ban.

"This is not about religion," Trump said in the statement issued Sunday evening. "This is about terror and keeping our country safe. There are over 40 different countries worldwide that are majority Muslim that are not affected by this order."

He also tweeted on the issue early Monday.

Only 109 people out of 325,000 were detained and held for questioning. Big problems at airports were caused by Delta computer outage,..... — Donald J. Trump (@realDonaldTrump) January 30, 2017

protesters and the tears of Senator Schumer. Secretary Kelly said that all is going well with very few problems. MAKE AMERICA SAFE AGAIN! — Donald J. Trump (@realDonaldTrump) January 30, 2017

There is nothing nice about searching for terrorists before they can enter our country. This was a big part of my campaign. Study the world! — Donald J. Trump (@realDonaldTrump) January 30, 2017

If the ban were announced with a one week notice, the "bad" would rush into our country during that week. A lot of bad "dudes" out there! — Donald J. Trump (@realDonaldTrump) January 30, 2017

Advocacy and aid groups have condemned Trump's order as a "Muslim ban" as lawyers for the American Civil Liberties Union and other organizations continued to work to help immigrants enter the country as well as obtain clarity around whether the ban applied to legal permanent residents.

Trump's statement denies that the executive order constitutes a religious test, claiming that "the media" had falsely reported that the travel restrictions targeted Muslims. His executive order does "prioritize refugee claims made by individuals on the basis of religious-based persecution, provided that the religion of the individual is a minority religion in the individual's country of nationality" in Muslim-majority countries.

Critics who argue that the ban is religion-based point to statements Trump and advisers have made as proof. In an interview with Christian Broadcasting Network, Trump said he would prioritize Christians. Trump adviser Rudy Giuliani, meanwhile, told Fox News Saturday night said that Trump called to ask him for "the right way to do it legally," referring to what Giuliani called a "Muslim ban." While on the campaign trail, Trump called for a "total and complete shutdown of Muslims entering the United States," a position still listed on his website.

Trump on Sunday also defended his executive actions by saying that the Obama administration had previously identified the same seven countries "as sources of terror." But that claim is misleading, as Congress and the Obama administration together designated the seven nations as dangerous for American citizens to visit. They were not designated as a source of immigrant-related terrorism.

Arizona Sen. John McCain, chairman of the Senate Armed Services Committee, and South Carolina Sen. Lindsey Graham criticized the order, saying that it would send the wrong message to the country's most integral allies, many of whom are Muslim.

"Our most important allies in the fight against ISIL are the vast majority of Muslims who reject its apocalyptic ideology of hatred," the two Republican senators said in a joint statement. "This executive order sends a signal, intended or not, that America does not want Muslims coming into our country. That is why we fear this executive order may do more to help terrorist recruitment than improve our security.”

Trump then took to Twitter to attack the two longtime senators.

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The joint statement of former presidential candidates John McCain & Lindsey Graham is wrong - they are sadly weak on immigration. The two... — Donald J. Trump (@realDonaldTrump) January 29, 2017

...Senators should focus their energies on ISIS, illegal immigration and border security instead of always looking to start World War III. — Donald J. Trump (@realDonaldTrump) January 29, 2017

Meanwhile, the American Civil Liberties Union, assisted by immigration and refugee groups, have successfully brought multiple suits forward to curb Trump’s executive order that restricts the access of travelers from seven Muslim-majority nations — Syria, Iraq, Iran, Sudan, Libya, Somalia and Yemen.

"We have been able to curb the immediate and disturbing consequences of an unconstitutional and unconscionable executive order,” said Marielena Hincapie, executive director of the National Immigration Law Center.

Related: Merkel: Terror Fight Does Not Justify Trump Immigration Ban

The original ruling against the executive order came from a federal judge in New York who said that those who arrived in the United States legally from the seven nations could not be deported. This applied to visa and green card holders alike and is a nationwide injunction.

The ACLU with the help of refugee and immigrant rights groups in Massachusetts and Virginia were able to gain additional footholds beyond the baseline order made in New York. In Boston, two federal judges placed a restraining order on Trump’s travel ban that will last for at least seven days. In Virginia, lawyers earned the right to meet with detainees and the DHS and Customs and Border Protection were forbidden from deporting legal immigrants for a week.

There have been some attempts for clarity about how the executive order affects various immigrant groups. One senior White House official told NBC News Saturday evening that legal permanent residents of the U.S., or green card holders, would be exempt from the executive order.

White House Chief of Staff Reince Priebus seemed to affirm that idea on "Meet the Press" earlier in the day.

However, the Trump administration and the Department of Homeland Security also pushed back on the rulings.

A senior White House official said earlier Sunday that the president had the right and Constitutional power to enact the order. According to the official, the judge’s decision changed nothing.

“All stopped visas will remain stopped. All halted admissions will remain halted. All restricted travel will remain prohibited,” the official said. “The executive order is a vital action toward strengthening America's borders, and therefore sovereignty. The order remains in place."

With the federal judges' ruling appearing to conflict with the executive order, uncertainty and chaos continued across the nation as lawyers sought access to those detained at airports and reports rolled in that Customs and Border Patrol agents were not abiding by the federal ruling.

Impromptu legal aid stand @dulles_airport, where lawyers say Customs officers refusing to comply with court orders. pic.twitter.com/wXFdnDFzGv — Matthew Rosenberg (@AllMattNYT) January 29, 2017

"The [judge’s ruling] is a blanket order for everyone that is affected by the Trump order no matter what status they’re in," said Lee Gelernt, deputy director of the ACLU Immigrants’ Rights Project, who argued the New York case.

“None of them can be removed from the U.S. while the judge determines the legality of the" executive order, he added.

Gelernt said the struggle for the ACLU and the groups that are assisting is that they do not know where all the affected immigrants are. The judge’s ruling also said the federal government is expected to provide a list of all immigrants who are being detained.

More than 16 hours later, the government still had not provided that list.

According to the temporary restraining order, the ACLU had “met their burden” of proving that there is a “strong likelihood” that detaining these immigrants would be unconstitutional because it violates their rights to Due Process and Equal Protection.

Photo Gallery: Ban Sparks Protests at Airports Across the Nation

It is unclear whether the additional rulings apply nationwide.

Gelernt said these cases against the executive order would continue. The group is seeking to have a judge rule it unconstitutional, he added.

Hincapie doubled down and said more than 2,000 lawyers across the country have organized themselves to help in an ongoing basis. This, she said, would only be the beginning.

“The president thinks this will go away quickly … we can assure the administration and all of you that this is not the case,” she said to a group of reporters.

State and city officials were quick to share their displeasure with Trump's executive order.

Sixteen state attorney generals committed in a shared statement to battle the order.

"As the chief legal officers for over 130 million Americans and foreign residents of our states, we condemn President Trump's unconstitutional, un-American and unlawful Executive Order and will work together to ensure the federal government obeys the Constitution, respects our history as a nation of immigrants, and does not unlawfully target anyone because of their national origin or faith," the group wrote.

From New York to Los Angeles, mayors of major cities, where most of the detained immigrants were being held, condemned the executive order. Many said that it directly opposed American ideals.

Philadelphia Mayor Jim Kenney went one step further and said that the Philadelphia International Airport would allow future passengers despite the executive order.

“We’re proud to announce that in addition to the release of anyone detained at the airport yesterday afternoon, all new passengers arriving today will be treated the same as they would have been prior to the executive order," he said in a statement.

Protests appeared at airports across the country after people heard that the travel ban had taken an immediate effect and that people were being detained.

"The community support from everyone in New York and around the country is absolutely critical," Gelernt said. "Any successful civil rights movement needs the technical lawyering in court and the enormous support from the public."