In the latest twist in a long legal saga, a spokesman for the Constitutional Court said its chief judge had "issued a temporary order to halt the implementation of all rulings that were issued over the Tiran and Sanafir accord".
The spokesman, Ragab Selim, told AFP the suspension would last until the court could determine which of the legal rulings in the case "will be implemented and which was issued by the institution with jurisdiction".
Egypt's parliament approved the transfer of the islands to Saudi Arabia on June 14 despite significant public opposition.
The deal sparked rare street protests after it was signed last year, with President Abdel Fattah al-Sisi accused of having sold the islands to Saudi Arabia.
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A lower court had ruled that the transfer would be illegal, a decision that was upheld by Egypt's Supreme Administrative Court but declared invalid by another judicial body, the Court for Urgent Matters.
Sisi on Tuesday again stressed "the need to return rights to owners" when it comes to the two islands, which Cairo says belong to Saudi Arabia and were leased to Egypt in the 1950s.
Lying at the mouth of the Gulf of Aqaba, the islands can be used to control access to the Israeli port of Eilat.
They were captured by Israel in the 1967 Middle East war before being returned to Egypt under the 1979 Camp David Accords.