Flydubai apologised after passengers on a flight from Israel experienced delays on arrival in Dubai.
The airline said it would review "the processes and procedures to prevent any delays to subsequent flights".
Israeli news reports and social media images showed what was later confirmed to be 155 people queueing in an arrival hall on Monday morning.
Reports said there had been an issue with entry visas since Sunday night.
Passengers were later allowed to pass through the airport and continue on their way.
State news agency Wam, which carried flydubai's statement, said "the policy permitting the entry of Israeli citizens remains unchanged, and Israeli citizens continue to be welcomed to the UAE".
Israel's foreign ministry spokesman Lior Haiat told Israeli media the issue apparently stemmed from confusion over whether the passenger or the travel company needed to secure the visa.
Israeli tourists began arriving in the Emirates last month, just weeks after the landmark Abraham Accord normalised relations between the two countries.
Flydubai and Israir are among the airlines to operate daily services between Tel Aviv and Dubai, allowing hundreds of UAE residents and Israelis to travel for holiday and business.