The announcement to suspend flights came two days after Tunisian government officials said the UAE had banned Tunisian woman from flying to or transiting through its territory.
Tunisia on Sunday suspended Emirates Airlines after a public outcry over "security" measures in the United Arab Emirates targeting women from the North African country.
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 international law and agreements".
A number of Tunisian women had said their travel to the Gulf state on UAE airlines had been delayed and some had been forced to undergo additional examination of their visas.
That triggered angry reactions on social media and media outlets in Tunisia.
The United Arab Emirates said Sunday that "security information" had caused the delays of Tunisian women from boarding flights to the Gulf state.
"We contacted our Tunisian brothers about security information that necessitated taking specific procedures," UAE Minister of State for Foreign Affairs Anwar Gargash said on Twitter.
"We highly value Tunisian women and respect them," he said, without elaborating.
The Tunisian government said on Friday it had asked the UAE ambassador for clarification, adding the envoy said the decision was for only a short period and the restrictions had been lifted.
Despite the clarification, Tunisian rights groups issued a statement on Saturday condemning the UAE measures as "discriminatory and racist".
Tunisia has been trying to repair diplomatic ties with the UAE which were damaged by its 2011 revolution and after the Muslim orientated party Al-Nahda, which has strong links with Qatar, came to power in the North African country.
Relations between Qatar on the 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.