"So far we have evacuated around 2,500... we don't have exact statistics but between 5,000 and 10,000 people" are still waiting to leave, he said at a news conference after meeting Tunisia Prime Minister Mehdi Jomaa.
Shoukri did not specify how long it will take to repatriate all the Egyptians, though Cairo promised on Saturday to take home about 2,000 people a day by air and if necessary by sea.
The Egyptians are stuck on the Libyan side of the border with Tunisia after the government there said it would only let in people other than Tunisians and Libyans if they could prove arrangements were in place to get them home.
On Friday, hundreds of Egyptians tried to storm the Ras Jedir border crossing into Tunisia, prompting Libyan border guards to fire warning shots.
Signup to our newsletter and follow us on Facebook and Twitter!
Tunisia said it would not be opening a camp to accommodate Arab and Asian workers fleeing Libya as it did in 2011 during the civil war which led to the overthrow of long-time dictator Moamer Kadhafi.
This time Tunis asked each state to organise the repatriation of its citizens, only letting them enter the country as and when transport became available.
Since mid-July, Libya has seen deadly clashes between rival militias in Tripoli and the eastern city of Benghazi.
Tripoli airport has been closed since gunmen, mostly Islamists, attacked it on July 13 in a bid to wrest control from the Zintan brigade of former rebels who have held it since the 2011 revolt.