It flies daily to 11 US cities.
Reuters reports the ban also applies to pilots and flight attendants from those seven countries, even though all flight crew who are not United States citizens already need a special visa to enter the country.
US and global airline industry seems to have taken a big blow as President Donald Trump announced travel restrictions on seven Muslim countries.
Another Emirates spokeswoman said the impact of the ban on operations would be minimal.
"For passengers who are looking for more information, we encourage them to contact the US Consulate or visit the US Customs and Border Protection website".
Other airlines were informed about the new rules in conference calls with USA authorities. The airline added that it is offering refunds and rebooking passengers "where permitted".
Trump took to Twitter on Monday to defend the abrupt order. Passengers are responsible for ensuring they have the required documents for their travel.
For example, Britain's foreign office said it had been informed by the USA government that travel restrictions did not apply to people travelling from the United Kingdom regardless of their nationality or place of birth.
Airlines and airports in Dubai, Germany, France and Amsterdam each said on Monday a small number of passengers had been prevented from boarding flights to the United States as a result of the new rules.
A spokesman for Germany's Lufthansa said an aid organisation had not been allowed to bring refugees to the United States via Frankfurt.
An Etihad Airways spokesman said: "We are continuing to work closely with US Customs and Border Protection agency both here in Abu Dhabi and in the US on the immigration issues presented over the weekend".
Japan Airlines earlier planned to consult US authorities about passengers planning to travel with passports of the seven countries, but the carrier later made a decision to bar such passengers from boarding, except those with diplomatic visas, following a notification from the International Air Transport Association, JAL officials said.
All pilots and flight attendants who are non-US citizens need visas to pass through U.S. immigration, but any staff who hold passports issued by the seven affected countries - Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen - are unable to enter the country, whether they already have the necessary visa or not.
German business travel association VDR said the new US policy was damaging for business and harmed the image of the United States overseas.