A US judge has issued a temporary halt to the deportation of visa holders or refugees stranded at airports after President Donald Trump issued an order barring entry to them for 90 days.

The American Civil Liberties Union, ACLU, filed a case in response to the order issued on Friday, saying that an estimated 200 people were being held at airports or in transit.

The ruling from federal Judge Ann Donnelly, in New York, prevented the removal from the US of people with approved refugee applications, valid visas, and “other individuals… legally authorised to enter the United States”.

Donelly held that there was a risk of “substantial and irreparable injury” to those affected.

The case was brought early on Saturday on behalf of two Iraqi men detained at JFK Airport in New York.

One worked for the US military in Iraq. The other is married to a former US military contract employee.

Both have now been released while another court hearing is set for February.

Thousands of people have been protesting at US airports over Trump’s clampdown on immigration.

His executive order halted the entire US refugee programme and also instituted a 90-day travel ban for nationals from Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen.

Those who were already mid-flight were detained on arrival – even if they held valid US visas or other immigration permits.

Defending his move, President Trump early on Sunday tweeted: “Our country needs strong borders and extreme vetting, NOW.”

On Saturday, amid protests and court challenges, he told reporters the order was “working out very nicely. You see it at the airports, you see it all over.”

Other executive orders issued by Trump on Saturday include: a ban on administration officials ever lobbying on behalf of a foreign government; an order to Defence Secretary Jim Mattis to come up with a plan within 30 days to defeat so-called Islamic State; restructuring the National Security Council with a key role for Steve Bannon, the former populist right-wing media executive who is now Trump’s top strategist.

Judge Donelly’s ruling, however is not on the constitutionality of Trump’s executive order and it remains unclear what will happen to the people who are still stranded at US airports.

In its response, the Department of Homeland Security said it would continue to enforce the measures that on Saturday had affected “less than 1% of the more than 325,000 international air travellers who arrive everyday”.

It added that the US government “retains its right to revoke visas at anytime if required for national security or public safety”.

A Syrian scientist working on skin cancer research and currently residing in Germany, who as a result of the ban can no longer travel to Philadelphia in February to visit colleagues said that “the feeling of injustice is so big, and this ban is so demeaning! Shame!”

Another Jordanian cardiology fellow whose Syrian wife’s family cannot come to visit in the US, described the ban as “Dreams shattered,” while an Iranian professional in Washington DC, whose wife is now stuck overseas noted that “we may try our chances with other countries.”

Lee Gelernt, deputy legal director of the Immigrants Rights Project, who argued the case in court said that some people had been threatened with being “put back on a plane” later on Saturday.

Gelernt also said the judge had ordered the government to provide a list of names of those detained under the order.

Judges elsewhere in the US have also ruled on the issue. In Boston, a judge decided two Iranian nationals, professors at the University of Massachusetts, should be released from detention at Logan International Airport.

Similarly, an order issued in Virginia banned, for seven days, the deportation of green card holders held at Dulles Airport and ordered the authorities to allow access to lawyers Amid all the controversy, President Trump tweeted that his directive was “not a Muslim ban, but we’re totally prepared.”

Criticism of Trump’s decision has been growing louder outside the US.

Iran and Iraq are threatening a reciprocal ban on US citizens entering the country.

Chancellor Angela Merkel of Germany issued a statement saying “even the necessary, determined fight against terrorism does not justify placing people of a certain origin or belief under general suspicion”.

Canadian Prime Minister Justin Trudeau tweeted that his government remained committed to welcoming “those fleeing persecution, terror and war”.

A spokesperson for UK Prime Minister Theresa May said she “did not agree” with the restrictions, and French independent presidential candidate Emmanuel Macron tweeted: “I stand with the people fleeing war and persecution”.