Two people were killed in Salloum, near the Libyan border, in clashes between protesters and armed forces, said the website of the state-run daily Al-Ahram.
The clashes erupted Tuesday evening after protesters tried to block the international road between Egypt and Libya.
The residents were protesting higher fees on trucks crossing the road, which pushed the army to intervene to open the road.
Anwar Abdel Maksoud, 14, and Abdel Moula Mahmoud Beshry, 23, were shot dead by army units, the paper said.
Some 200 people blocked the road on the Salloum plateau, protesting the higher fees crossing into Libya, which were raised from LE450 to LE600.
Calm was restored after security forces took over the city.
State-run news service MENA cited a security source as saying the youth in Salloum refused to abide by transportation and trade procedures at the border, creating problems at the border crossing, hindering its work and the application of the law.
Translated from Al-Masry Al-Youm