The move comes days after Shafiq, in exile in the UAE since 2012, announced his candidacy in next year's election and then said he was being prevented from leaving the country, angering his Emirati hosts.
Shafiq, a former army general appointed as prime minister by Hosni Mubarak, had narrowly lost an election to Islamist president Mohamed Morsi in 2012, a year after Mubarak's overthrow.
He was placed on trial after the polls on corruption charges and acquitted, and one of Shafiq's lawyers said last year that he was free to return to Egypt.
One aide said she witnessed officials arriving at the house and was told that Shafiq, seen as a main challenger to President Abdel Fattah al-Sisi, would be deported to Egypt on board a private plane.
"They took him from the house and put him on a private plane. They said he would go back to Cairo, because they can deport him only to his home country," she said.
Another aide confirmed to AFP that he would be deported to Cairo, and his lawyer Dina Adly wrote on Facebook that Shafiq had been "arrested" to be sent home.
After he announced his candidacy on Wednesday, pro- government media and some officials assailed Shafiq, who is seen as the only challenger to Sisi with even a remote chance of winning a large number of votes.
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