The protesters were arrested on Monday during a demonstration in central Cairo against the transfer of Tiran and Sanafir islands to Saudi Arabia.
The 12 are accused of holding a protest without informing the interior ministry.
The detained protesters are also under investigation over accusations of attacking police forces and destroying public property.
The transfer of the islands was part of a maritime border accord signed between Riyadh and Cairo during an April visit by Saudi Arabia’s King Salman to Egypt.
On December 29, 2016, the Egyptian government endorsed the contentious deal and sent it to the parliament for ratification.
The accord is being disputed in Egyptian courts, but the government has put its weight behind approving the deal. The government argues that the islands basically belonged to Saudi Arabia, but they were leased to Egypt in 1950s.
Back in June, Egypt’s Higher Administrative Court had annulled the deal, saying Egyptian sovereignty over Tiran and Sanafir could not be given up.
However, the government of President Abdul Fattah Al Sissi lodged an appeal to suspend the execution of the June ruling.
In late December 2016, Cairo’s appeal court approved a verdict by a lower court that rejected the June ruling by the administrative court. A more senior tribunal is due to deliver a verdict on January 16.
The deal has triggered unprecedented mass demonstrations with protesters slamming the arrangement as unconstitutional.
Demonstrators and critics have accused Sisi of surrendering Egyptian territory for money, with reports saying Cairo is receiving 20 billion dollars in aid from Riyadh in return for agreeing to relinquish sovereignty over the islands.
The uninhabited islands of Tiran and Sanafir lie about 4 kilometers apart in the Red Sea. They are situated in the narrow entrance to the Gulf of Aqaba leading to Jordan and the occupied Palestinian territories, Press TV reported.