A court in the US has issued an emergency stay halting deportation under US President Donald Trump's executive order that bans citizens from seven Muslim majority countries from entering the country.

New York: A court in the US has issued an emergency stay halting deportation under US President Donald Trump's executive order that bans citizens from seven Muslim majority countries from entering the country.

The federal court for the Eastern District in New York on Saturday issued the order preventing the government from sending immigrants back to their home countries as it would cause them "irreparable harm".

It is unclear yet if they would remain in detention until a substantive ruling on the constitutionality of the ban is delivered. "If someone is not being released, I guess I'll just hear from you," The New York Times quoted Judge Ann Donnelly as saying.

The order comes as American Civil Liberties Union early on Saturday filed a lawsuit in response to the "extreme vetting", BBC reported.

Trump's executive order halts all immigration from Iraq, Iran, Libya, Somalia, Sudan, Yemen, and Syria.

The ban lead to widespread confusion about how it would be implemented and enforced.

According to the group, between 100 and 200 people are being detained at airports or in transit.

Hundreds of people protested at airports across the country over the new President's clamp down on immigration.

Lee Gelernt, deputy legal director of the Immigrants Rights Project, argued the case in court and was greeted by a cheering crowd outside.

He said some people had been threatened with being "put back on a plane" later on Saturday.

"This is a remarkable day," said the ACLU's executive director, Anthony Romero.

"On day one after he signed the executive order, we took him to court... that it was unconstitutional, it was un-American, and it flew in the face of established statutes that we have long regarded in this country."