The federal government's top lawyer, US Acting Attorney General Sally Yates had said Justice Department would not defend new travel restrictions targeting seven Muslim-majority nations.
This was because she was not convinced they were lawful.
Trump's directive on Friday put a 120-day hold on allowing refugees into the country,
He also placed an indefinite ban on refugees from Syria. Also included is a 90-day bar on citizens from Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen.
The White House dismissed her comments as rhetoric and said Trump acted within his presidential powers.
There have been only a handful of instances in US history of top Justice Department officials publicly breaking with the White House.
The most famous example was in 1973, when then-Attorney General Elliot Richardson resigned. He refused to obey President Richard Nixon's order to fire a special prosecutor investigating the Watergate scandal.
An internal Department of Homeland Security document showed 348 visa holders were kept from boarding US-bound flights this week. More than 200 people came to the United States but were denied entry.
More than 735 people were pulled aside for questioning by US Customs and Border Protection officers in airports, including 394 green card holders, who are legal permanent residents of US.
The Council on American-Islamic Relations, the country's biggest Muslim advocacy group, filed a federal lawsuit on behalf of more than 20 people.
Technology companies Amazon.com Inc and Expedia Inc , both of which are based in Washington state's Seattle area, will support the state's suit.
Microsoft Corp, said it has been cooperating with the attorney general's office to provide information about the order's impact to be supportive.
Other companies also went public with concerns, including the chief executives of Goldman Sachs Group Inc and Ford Motor Co.
The Iraqi parliament voted to ask the country's government to retaliate against the United States, putting at risk cooperation in the fight against Islamic State.
British Foreign Secretary Boris Johnson joined a chorus of concern expressed by US allies, ranging from Iraq to Germany.
