"I fulfilled my part, and it is now in the parliament and with the judiciary. We won't interfere," Sisi said live on television during a conference in the Suez canal city of Ismailiya.
The deal to hand over the islands, signed during an April 2016 visit by Saudi King Salman during which Riyadh showered Egypt with aid, provoked accusations in Egypt that Cairo had "sold" the strategic islands.
The accord has sparked street protests and a legal battle between the government, which insists along with Sisi that the islands are Saudi, and lawyers opposed to the measure.
"From the start, we told our (Saudi) brothers that we will go through procedures, but that we will not interfere with the technical side, and that the ratification will be done according to legal and constitutional rules," Sisi said on Wednesday.
Cairo said the two islands -- Tiran and Sanafir -- were Saudi territory to start with, but had been leased to Egypt in the 1950s, and Sisi has personally insisted publicly that the islands are Saudi.
The State Lawsuits Authority, the government's legal representative, has been battling in courts with lawyers opposed to the deal.
In June, an administrative court ruled against the transfer.
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That ruling was upheld in January by Egypt's top administrative court which sided with the arguments of Khaled Ali, the lawyer who had initially demanded for the transfer be blocked.
But on April 2, the urgent matters court in Cairo ruled that the highest administrative court's ruling was invalid.
The State Lawsuits Authority filed an objection and the advisory "State Commissioners Authority is currently preparing its report to be presented" in court, Ali told AFP Wednesday.
After that, the constitutional court will hear arguments by the two sides, Ali said.
At the same time, the government has sent the deal to the parliament.
On April 10, parliament speaker Ali Abdel Aal referred the deal to the Constitutional and Legislative Affairs Committee for deliberations.
"We, as the executive authority, have concluded our responsibility, finished it and submitted it," Sisi said on Wednesday.
Saudi Arabia has been a main financial backer of President Abdel Fattah al-Sisi since the former army chief toppled his Islamist predecessor in 2013.