Kenya’s election on December 27 returned Kibaki to power for a second five-year term, with official results putting Raila Odinga, the leader of the opposition Orange Democratic Movement, second.
Odinga accused Kibaki of stealing the vote.
About 685 people were killed as post-election violence swept across Kenya.
Foreign and local election observers have said the vote was deeply flawed.
Efforts at international mediation have so far failed.
Annan visit
Before Annan's arrival, Michael Ranneberger, the US ambassador, urged both sides to make a political settlement.
"The tragedy Kenya is now suffering, and the extremely bitter polarisation of Kenyan society, demands that all leaders and institutions speak in a responsible, respectful and dignified tone," Ranneberger said in a statement.
The election has tapped into resentments that resurface regularly at election time in Kenya but never has such a dispute lasted so long or cost as many lives.
Several people were beaten and hacked to death with machetes in a Nairobi slum over the weekend, residents said.
Opposition boycott
On Monday, Odinga called for a new vote after returning to his western stronghold for the first time since the election.
"People have been asking me to give them guns but I'm giving them votes," Odinga told supporters in Kisumu, about 225km from the capital.
As Kibaki becomes more entrenched each day, the opposition's best hope may rest in working out a power-sharing agreement that could make Odinga prime minister or vice-president.
Despite a ban Odinga called for another "peaceful protest" on Thursday.
Odinga has also urged supporters to boycott companies owned by Kibaki allies, including Equity Bank and bus companies CityHoppa and Kenya Bus.
The government has condemned the planned economic boycott as "sabotage".