Officials in Tunis have barred the carrier from touching down in the capital due after the airline stopped the country's women from flying to or transiting through the UAE at the weekend.
Emirates said it would stop operating its Dubai-Tunis connection following instructions from the North African country.
On Friday, the Tunisian government added that it had asked the UAE ambassador to clarify what was happening and had been told that the measures were temporary and had already been lifted.
That triggered angry reactions on social media and media outlets in Tunisia. The reason for this ban is that some Tunisian women were not allowed to board the flights of Emirates, thus causing this issue.
"We have contacted our Tunisian brothers about security information that necessitated taking specific and circumstantial measures", Gargash said on Twitter.
Tunisia's transport ministry said in a statement 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". "In the UAE, where we are proud of our experience in empowering women, we appreciate Tunisian women, respect them and value their pioneering experience", the tweet read. "We will avoid attempts at misinterpretation and misrepresentation".
Meanwhile, according to Al Ain news, Tunisian presidency spokesperson Saeeda Qureshi said, "The measures that the UAE took regarding travel of Tunisian women, are considered part of their sovereignty procedures, and not a sign of a trust crisis between the two countries".
The move comes amid widespread anger in Tunisia, with rights groups condemning it as being racist and discriminatory.