The suspension, which will take effect on December 25, 2017, comes after several Tunisian women were denied boarding for their Dubai-bound flights on Emirates.
A Tunisian official said UAE authorities had received "serious security information about the possibility of a terrorist attack" by female Tunisian passport holders. He added: "The Tunisian woman has exposed their failings once again; suddenly many of them have become dumb and abandoned their pens, while human rights activists have suddenly disappeared".
The UAE said "security information" had caused the delays.
On Friday, Tunisia's state-run news agency, Salem Zeabi, reported that the UAE ambassador to Tunisia, was called to the Ministry of Foreign Affairs to "provide clarification on the measure banning" Tunisian women from flying to or transiting through the Gulf state's territory.
All attempts of the Tunisian authorities to help their nationals in Tunis, Abu Dhabi and Beirut, made within the last several days, resulted in Emirates halting flights between Tunis and Dubai.
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Emirates confirmed in a tweet that it would stop flights between Dubai and Tunis today (Monday) until further notice, without giving a reason.
A Tunisian foreign ministry spokesman said Friday that the sudden ban would be dealt with "to maintain the dignity of Tunisians".
Tunisia has been making an effort to fix the otherwise strained diplomatic ties with the UAE.
Relations between Qatar on one hand and Saudi Arabia, the UAE, Bahrain, and Egypt on the other have been severed since June after the four Arab countries accused Doha of backing "terror" groups in the region, a charge denied by Qatar.