Israel had eased some of its restrictions on Gaza as part of a truce with Palestinian groups that began on Thursday, but made any opening of Rafah, the only crossing that bypasses Israel, conditional on a prisoner swap.
Egypt played a key role as mediator in brokering the ceasefire as Israel rejects direct contact with Hamas, which it blacklists as a terrorist group. Hamas in turn refuses to recognise the Jewish state.
The deal earned Olmert heavy domestic criticism for not making the truce conditional upon Hamas releasing Shalit, captured two years ago in a deadly cross-border raid.
The truce envisages freeing 450 Palestinian prisoners held in Israeli jails in exchange of Shalit.
Suleiman Awad, an Egyptian presidential spokesman, told the MENA news agency that the two leaders discussed Shalit.
"Egypt is continuing its efforts to reach a prisoner exchange deal between both sides.
"As for Rafah, there are constant contacts aimed at opening the crossing according to the protocol which was reached in November 2005.
"Egyptian efforts on this issue are continuing."
On arrival in Egypt, the Israeli premier hailed Egypt's mediation.
Mark Regev, an Israeli spokesman, said: "You cannot move to anything close to normalcy concerning the crossings before Gilad Shalit is released", adding that "there is no doubt" he is alive.
Shalit's parents asked Israel's Supreme Court on Sunday to instruct the state not to open the Rafah crossing before Gilad, 21, is released or before Hamas vows to release him.
The state prosecution said in its reply to the Supreme Court that following the agreement, "intensive talks" on a prisoner exchange deal were expected to begin this week.