Hundreds of Israelis who landed in the United Arab Emirates on Monday morning were denied entry due to changes in visa application procedure.
More than 160 passengers on board FlyDubai flight FZ1628, which departed from Tel Aviv at 1am, were held up at Dubai airport for over two hours.
The UAE's Foreign Ministry later said the passengers will be allowed to enter the country "in the coming hours" having filled the correct visa forms online at the airport.
The other two fights due to depart on Monday morning for Dubai have been delayed awaiting a resolution of the problem.
The Foreign Ministry earlier said it was in contact with its UAE counterparts in an effort to solve the problem.
One Israeli passenger told Ynet that he has been waiting for over two hours to be allowed in, despite being told by the airline their visas were all in order.
"There are small children and babies here all after a sleepless night," he said. "We paid hundreds of shekels for this flight but there are no representatives of the airline and anyone carrying an Israeli passport is being denied entry."
Another passenger claimed FlyDubai representatives were warned there would be problems upon arrival but ignored the warning. "They are trying to work things out but so far without success," he said.
A FlyDubai spokesperson later issued a statement, apologizing for the incident.
"We are reviewing the reasons behind the entry delay and fully understand that this was inconvenient for our passengers," said the statement. "This is not the standard of service we expect for any of our passengers and we are also revalidating the processes and procedures to prevent any delays to subsequent flights."
Israir CEO Uri Sirkis said problems with entry visas for Israelis began on Sunday when four of the airliner's flights arrived in the emirates. "The Foreign Ministry was able to sort things out," he said. "We have delayed our departure this morning until we are sure our passengers will be allowed in."
Israel and the UAE reached a mutual agreement two weeks ago, to allow citizens in to their respective countries without the need of a special entry visa for a period of time until an official agreement signed in October comes into effect.