Mohammed Mursi passed a decree earlier this week granting himself extensive new powers.
It includes a bar on any court dissolving the constituent assembly, which is drawing up a new constitution.
Thursday’s decree has sparked angry demonstrations, with attacks on offices of Mohammed Mursi’s Muslim Brotherhood party.
The president has said he is acting to protect the revolution.
In a statement, the Supreme Judicial Council called on Mohammed Mursi to “this decree from everything that violates the judicial authority,” Mena state news agency reported.
There had been reports that the council was about to disband the constituent assembly for a second time.
That could seriously derail the transition to democracy, says our correspondent, further delaying new parliamentary elections, which could deter Egypt’s political leaders from taking tough decisions while they wait for the vote.
Mohammed Mursi also sacked his prosecutor general on Thursday and gave himself the sole power to appoint a new one.
His replacement moved quickly to reopen criminal investigations into ousted President Hosni Mubarak, his family, and former regime officials.
It is likely to be a popular move, as although Mubarak is serving a long jail term for ordering the killing of protesters during the 2011 uprising, many officials were acquitted, creating deep resentments.
The ruling also bans any challenging of the president’s decisions and laws.
Both critics and supporters of Mohammed Mursi have staged rallies since the decree. Overnight, crowds gathered in Cairo’s Tahrir Square, vowing to stage a sit-in.
A large opposition rally is also planned for Tuesday.
The US said earlier that Mohammed Mursi’s move had raised concerns in the international community.
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