No one commented before the closed-door session began inside Kibaki's office in Nairobi, the Kenyan capital.
Earlier in the day, Annan met Kibaki amid fresh clashes that have killed at least 12 people, adding to a death toll of nearly 800 in post-election violence.
Annan held talks with Odinga on Wednesday.
Odinga, at Annan's request, called off mass rallies scheduled for Thursday in protest against the disputed election.
Thursday's Kibaki-Odinga meeting raises hopes after a human-rights watchdog accused ODM officials of organising tribal violence in the Kenya's Rift Valley, backing up government allegations.
Annan is leading a panel of African leaders urging Kibaki and Odinga to open negotiations to end a crisis that has displaced a quarter of a million people in addition to the deaths and material damage.
Police had banned Thursday's rallies after clashes at demonstrations last week killed 80 people.
Yoweri Museveni, the Ugandan president who was among the first leaders to recognise Kibaki's legitimacy after the contested poll, also met Kibaki on Wednesday.
However, several international attempts to bring the two sides into face-to-face talks have so far failed.
Riot police and protesters on Wednesday fought running battles at a funeral procession held by the opposition for slum residents killed in violence in Nairobi.
Odinga fled from the scene of the clashes.
He later said in a statement: "This government first committed the unforgivable crime of stealing the vote, it then kills those who protest, and finally, when people come to mourn the departed, it assaults them as well.
"This latest attack on a peaceful gathering shows that this government is running amok ... To assault peacefully gathered mourners is a terrible crime, made much worse when the peoples' leaders, including the winner of the presidential election, are the targets."
Separately, at least 12 people were killed in Kenya in overnight fighting between rival tribes and gangs, police said on Thursday.
Six were hacked to death in Kaptembwa and two others in Bahati, two settlements near the town of Nakuru, northwest of Nairobi, a police commander said.
Police shot dead two men in the central town of Limuru when members of Kibaki's Kikuyu tribe started evicting residents from rival tribes from their homes, he said.
In Kariobangi, a slum in Nairobi a man was hacked to death in tribal-gang violence.