The transport ministry said the measure would stay in place until Emirates was able to "operate flights in accordance with law and international agreements".
The UAE said "security information" caused the delays.
"We contacted our Tunisian brothers about security information that necessitated taking specific procedures," Emirati Foreign Minister Anwar Gargash said on Twitter on Sunday.
"We highly value Tunisian women and respect them," he added.
Tunisian government officials said the UAE had banned Tunisian women from flying to or transiting through its territory.
On Friday the Tunisian government said it had asked the UAE ambassador to clarify what was happening and had been told that the measures had been temporary and had already been lifted.
Local media reported that Tunisian women had been blocked from boarding Emirates flights to Dubai over several days.
According to AFP news agency, some Tunisian women said their journeys to the UAE had been delayed and some that their visas had to undergo additional examination.
Tunisia has been trying to improve relations with the UAE that were damaged by its 2011 revolution.
Tunisia's ruling Ennahda party also has links to Qatar, which has been cut off by the UAE, Saudi Arabia and Bahrain over its alleged support for terrorism.
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