A Cairo court ruled that the Egyptian government must destroy all tunnels between Egypt and the Gaza Strip.
The labyrinth of tunnels is an infamous smuggling route for arms trafficking.
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It is also believed that 30% of the goods that reach the Gaza Strip, as well as over 1.5 million people a year, make their way through the tunnels in an attempt to bypass the blockade that has been imposed by Israel and Egypt for more than seven years.
The underground maze stretching beneath Rafah, Sinai and Gaza is said to include 450 main tunnels and 750 sub-tunnels.
Egypt's ruling Muslim Brotherhood has close ties with the Hamas Islamists that run Gaza, but many Egyptians fear the enclave is a security risk for Egypt. Leftist lawyers said they brought the case with activists to force the government's hand.
Egyptian President Mohamed Morsi's national security adviser Essam Haddad said that Egypt will not tolerate the two-way flow of smuggled arms through the tunnels, adding that it is destabilizing its Sinai Peninsula.
Egyptian forces flooded some of the tunnels earlier this month.
"The court ruled to make it obligatory that the government destroy the tunnels between Egypt and the Gaza Strip," Judge Farid Tanaghou said.
"I filed the case because I was worried about the state of national security in my country after the rise of the Muslim Brotherhood to power and its unclear policies and links with Hamas," said Wael Hamdy, a lawyer who brought the case.
He said the case had been brought after 16 Egyptian border guards were killed last August by militants near the Gaza border that highlighted lawlessness in the Sinai desert region adjoining Israel and Gaza.
Cairo said some of the gunmen had entered Egypt through the Gaza tunnels, an accusation denied by the Palestinians.
Dozens of tunnels have been destroyed since that incident, but, according to Hamdy, 2,000 are still open.
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