A judicial source told AFP news agency that the court issued the verdict on Saturday, a ruling seen as keeping with a systematic crackdown on Islamist groups by President Abdel Fattah el-Sisi.
The verdict resulted from two separate private suits filed by two lawyers against the de facto rulers of the Gaza Strip.
In an interview with Al Jazeera, Ghazi Hamad, a deputy foreign minister, rejected the court decision as "very dangerous."
"They are now saying that the [Palestinian] resistance and struggle against the occupation is a crime," he said.
Mustafa Barghouti, a senior Palestinian official who is neither from Hamas or Fatah, told Al Jazeera in a separate interview that the verdict "is a very unwise decision" that carries political complication.
"Hamas is part of the Palestinian national unity movement, and this decision is not useful."
Saturday's ruling comes just days after Egypt adopted a new anti-terrorism law allowing the authorities to close the premises of any declared "terrorist" organisation, and to freeze its assets as well as those of its members.
The relationship between Egypt's authorities and the Hamas has soured since the ouster of the Muslim Brotherhood’s Mohamed Morsi in July 2013.
Hamas is an offshoot of Egypt's Muslim Brotherhood, which Egypt also banned since the military coup in 2013.
Since then, Egyptian authorities have accused Hamas of aiding armed groups, who have waged a string of deadly attacks on security forces in Egypt's Sinai Peninsula.
In January, an Egyptian court also declared Hamas' armed wing al-Qassam Brigades a "terrorist" group.
The case was based on allegations that al-Qassam staged attacks to support the Muslim Brotherhood, and carried out deadly operations in the Sinai Peninsula in October 2014, allegations that the group denied.
Armed groups in Sinai have killed scores of policemen and soldiers since Morsi's overthrow, vowing revenge for a crackdown on his supporters that has left more than 1,400 people dead
ALJAZEERA