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".
"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 should avoid misleading attempts... We highly value Tunisian women and respect them," he said, without elaborating.
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 damaged by its 2011 revolution and after the Islamic party Al-Nahda, which has strong links with Qatar, came to power in the North African country.
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.