The comments came as the Libyan army denied reports of the imminent fall of Tripoli to forces led by renegade commander Khalifa Haftar.
President el-Sisi said in televised comments on Sunday the internationally recognised Government of National Accord (GNA) “is not able to have a free and real will because they have been taken hostage”.
He did not elaborate and there was no immediate comment from the Tripoli authorities.
El-Sisi said the Libyan conflict posed a threat to Egypt’s national security because fighters and weapons spill over the border into Egypt. He said Cairo had a right to interfere in Libya “but did not take this step to maintain the relationship and brotherhood with the Libyan people”.
Haftar’s Libyan National Army (LNA), which supports a rival government in the country’s east, has besieged the capital since April, vowing to oust the GNA from power.
Libya descended into chaos after the 2011 civil war involving NATO air strikes ousted and killed longtime ruler Muammar Gaddafi.
On Monday, the Libyan army denied recent media reports that Tripoli could soon fall into the hands of Haftar’s forces.
Haftar announced the “zero hour” was near for the UN-backed government last week, and said a “total assault was expected by every free and honest Libyan”.
But GNA military spokesman Mohamed Qanunu told Anadolu news agency “the situation on the ground is still in our favour”.
“Civilians, however, are suffering as a result of air bombardment by the war criminal Haftar,” Qanunu said, accusing the general of using mercenaries from Africa and Russia in his attacks on Tripoli.
“Atrocities have been committed against civilians in Tripoli and its outskirts in recent months,” he added.
Last month, Turkey and the GNA reached deals on military cooperation and the maritime boundaries of countries in the Eastern Mediterranean.
Turkish President Recep Tayyip Erdogan reiterated on Sunday that Ankara would send troops to Libya if the GNA made such a request.
“We are more than ready to give whatever support is necessary to Libya,” Erdogan said on A Haber TV.
According to the agreement, Tripoli could request vehicles, equipment and weapons for use in army, navy and air operations. It also makes a provision for new intelligence sharing.