Last night, Emirates said it was suspending its flights to Tunisia indefinitely shortly after the Tunis government said it had banned UAE carriers.
The transport ministry was clear that they will not change the step taken unless Emirates "operate flights in accordance with law and worldwide agreements".
The transport ministry said it had "decided to suspend" Emirates flights to Tunis "until the airline is able to find the appropriate solution to operate its flights in accordance with global law and agreements".
The UAE said "security information" had caused the delays.
Salem Issa Elkattam Zeabi, UAE Ambassador to Tunisia, who was summoned to clarify the issue, said the ban was "circumstantial and related to security arrangements, and that it was lifted", the Tunisian foreign ministry said in a statement.
The build up to the suspended flights followed anger in Tunisia over repeated reports of Tunisian women being banned from boarding Emirate flights from Tunis to Dubai.
"We contacted our Tunisian brothers about security information that required taking specific procedures", Emirati Foreign Minister Anwar Gargash said via a Twitter post on Sunday.
"In the UAE, we are proud of empowering women, we appreciate Tunisian women, and respect them".
Speaking to Mosaique FM, a local Tunisian radio station, one of the women described her experience at the Tunis-Carthage International Airport on Friday.
"So the daughter and the mum stay in Tunisia but the husband and son can travel".
In a statement on Friday, Tunisia's Ministry of Transport said such actions were "illegal" and "contradictory to the regulations in force in global civil aviation".