This is Rice and Gates's first joint tour of the region.
At a news conference following the meeting with the ministers, Rice said she had discussed the challenges facing Lebanon and Washington's commitment to a two-state solution in Palestine.
Earlier, on her way to Sharm el-Sheikh, Rice said that "as security permits, we hope more states would undertake more diplomatic missions to Iraq".
She also appealed for Arab countries to further cut Iraqi debts.
"He who wants to make peace does not start out with an arms initiative which is dangerous for the region"
Walid Muallem, Syria's foreign minister
Arab diplomatic missions in Baghdad have scaled back their representation after a campaign of attacks and kidnappings.
On Monday, the US announced military aid worth more than $43bn to Egypt, Israel, Saudi Arabia and other Gulf states in an effort to boost its Middle East allies against Iran.
Egypt will receive $13bn in aid over 10 years while $30bn will go to Israel over the same period, Rice said.
Rice said that an unspecified defence aid package was allocated for Saudi Arabia and the Gulf states.
The Saudi package is expected to upgrade the country's missile defences and air force and increase its naval capabilities, a defence official said on Saturday.
Saudi Arabia and the other Gulf countries are likely to receive as much as $20bn over 10 years, he said.
Rice said: "This effort will help bolster forces of moderation and support a broader strategy to counter the negative influences of al-Qaeda, Hezbollah, Syria, and Iran."
Syria’s foreign minister called the US administration’s armaments deal "dangerous".
"He who wants to make peace does not start out with an arms initiative which is dangerous for the region," Walid Muallem said on Tuesday.
Tehran accused the US on Monday of creating fear and causing divisions in the Middle East by announcing the major package of arms deals.
Mohammad Ali Hosseini, Iran's foreign ministry spokesman, said: "America has always considered one policy in this region and that is creating fear and concerns in the countries of the region and trying to harm the good relations between these countries."
However, Nicholas Burns, the US undersecretary of state, characterised the deals as a continuation of existing policy.
"It's not as if we're introducing some new element in the region," he said. "Iran is a factor in this, but it wasn't the overriding factor."
He said he saw no conflict between the aid packages to Saudi Arabia and Egypt, whose governments have a long record of human-rights abuses, and the current administration's long-term goal of promoting democracy in the region, led by George Bush, the US president.