It also criticised the media for spreading what it described as "deliberate falsifications" about an alleged attack on the presidential contingent in Haiti.
Director-General in the presidency, Frank Chikane, said the decision that Mbeki should attend the celebrations was taken in light of South Africa and the continent's commitment to a process of African renewal - which also involved people of African origin living in other parts of the world.
"His presence there had nothing to do with supporting one group against another," he told reporters in Pretoria. It also formed part of a decision to boost relations between African countries and the Caribbean.
Democratic Alliance leader Tony Leon has accused Mbeki of "propping up yet another international outcast - and in the process misusing millions of taxpayers' rands". He described Haiti's president Jean Bertrand Aristide as "the Mugabe of the Caribbean", and lamented that country's human rights record.
Civil unrest in Haiti has left 37 dead and 92 wounded since September, with anti-government protesters calling for Aristide's resignation.
Chikane said "differences of opinion" in a country should not prevent it from celebrating its achievements.
"There is no reason, because there are differences, not to celebrate the bicentenary of the Haitian revolution".
Haiti gained independence from France 200 years ago, and became the world's first black republic.
Acting Foreign Affairs Minister Lindiwe Sisulu told reporters that Mbeki had reiterated South Africa's willingness to assist in mediation talks in Haiti.
"We hope that all South Africans, instead of carping and criticising, will support this endeavour".
Chikane said the media should be worried about its integrity following the publication of "lies" to the effect that a helicopter in Mbeki's contingent had been fired on.
Sisulu reiterated, "not even a single shot was fired at the South African contingent in Haiti". French news agency AFP on Friday quoted police spokesperson Senior Superintendent Selby Bokaba as saying Mbeki's advance protection team came under fire the day before - prompting the president to cancel a scheduled visit to the north-western city of Gonaives.
But government officials, including Bokaba, later denied this.
Bokaba reportedly said his initial reports had been wrong because of "difficulties in getting the correct information from Haiti due to communication problems".
In a statement issued yesterday, police confirmed that gunshots were fired in Gonaives - but none directly at the helicopter or the advance team.
Chikane said the decision not to attend Gonaives festivities was prompted by an eruption of violence in the city that was unrelated to any opposition party.
He added there was no resistance from the Haiti political opposition to Mbeki's visit.
"We had discussions with the opposition. They have problems with their president - not with us".
In fact, opposition politicians asked Mbeki to raise certain issues with Aristide on their behalf, Chikane said.
Regarding the logistics of the trip, Sisulu said the SAS Drakensberg was moored off-shore as a logistical back-up for South Africans rendering assistance to Haiti in the planning of the celebrations. It was not taken along because officials feared "a huge disaster".
She confirmed this was the first time that such a naval vessel had accompanied a president on a foreign trip.
The DA said the government appeared to be engaged in a "silly egg-dance over detail in order to try and put a brave face on the Haiti fiasco".
On Bokaba's apparent about-turn, it said: "One has to ask who among the police put out such an alarmist initial report or whether the truth is that a senior police officer has been told by the government to change the official version of events".
The question remained, the party said, why Mbeki saw it fit to associate with "another international pariah" and what possible benefit South Africa had gained from it. – Sapa.
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