Last week Egyptian and Libyan warplanes hit IS targets inside Libya after the jihadists released a video showing the beheadings of 21 Christians, most of them Egyptian.
Since then Egypt has urged the hundreds of thousands of Egyptians who work in Libya to leave and chartered planes to ferry them home from Tunisia.
At least 1,000 Egyptians who fled to Tunisia have been airlifted home since the first flight was set up on Friday, a spokeswoman for the Tunisian transport ministry said.
A Tunisian customs official said that an unspecified number of Egyptians were also waiting on the Libyan side of the border, hoping to cross the frontier.
In July last year, thousands of Egyptians fleeing violence in Libya were stranded for days at the border with Tunisia, as authorities refused to let them in until Cairo had arranged for their transport home.
Tunisia was flooded by expatriates fleeing Libya during the 2011 uprising that toppled and killed dictator Moamer Kadhafi, and struggled to cope with the massive exodus.
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