Riyadh is a key backer of Islamist rebels battling to overthrow Syrian President Bashar Assad. Egypt's government, which is deeply suspicious of Islamist movements throughout the region, says Assad's government will have to be part of a negotiated settlement.
Cairo is hosting a group of Syrian non-Islamist opposition factions next week. There are also plans for Riyadh to hold a Syrian opposition conference but no date has been set yet.
Local media in both countries say the dispute over Syria has caused discord between the two allies.
"There is no disagreement," he told reporters. "In Syria, we are all seeking to remove Bashar Assad from power after he lost his legitimacy, and we are all seeking to restore peace and stability in Syria. We are seeking to protect the government and military institutions in Syria to be able to deal with the challenges after the Assad regime."
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Saudi Arabia has given billions of dollars to Egypt since the military overthrew Islamist President Mohammed Morsi in 2013.
Shoukry denied reports that Egypt and Russia are working to come up with a new political initiative for a negotiated solution in Syria, but said there was ongoing coordination between Cairo and Moscow.
Shoukry said his government is working with the Russians to convince the Syrian government "of the need to take part in the political process along with different oppositions" supported by Russia, Egypt and Saudi Arabia.
He added: "We don't have to necessarily agree completely with the framework or the output."
Highlighting the divergence, al-Jubeir said the contacts with Moscow are primarily to "convince Russia to give up on Bashar or to exert efforts or use influence in Syria to convince Bashar to give up power as soon as possible.