At least 800 people have been killed in the western Ivory Coast city of Duekoue this week, the International Committee of the Red Cross (ICRC) has said.
They died in inter-communal violence in one district of the city, it added.
The head of the ICRC delegation in the country said the event was particularly shocking in its scale and brutality.
Mr Ouattara was internationally recognised as president last year after the electoral commission declared him the winner of a November run-off vote, but Mr Gbagbo also claimed victory and refused to leave office.
‘Fearing for their lives’
The ICRC said delegates and volunteers from the Ivorian Red Cross had visited Duekoue on Thursday and Friday to gather evidence of the killings, which are believed to have taken place on Tuesday.
“There is no doubt that something on a large scale took place in this city, on which the ICRC is continuing to gather information,” ICRC spokeswoman Dorothea Krimitsas told the AFP News agency.
She said the Red Cross representatives had “themselves seen a very large number of bodies”. They took 28 bodies to the local morgue and more would be removed in the coming days, she added.
“Everything seems to indicate that this was inter-ethnic violence.”
The head of the ICRC delegation, Dominique Liengme, said in a statement: “This incident is particularly shocking in its size and brutality.”
“The ICRC condemns direct attacks on civilians and reminds the parties to the conflict to make sure that people in the territory under their control must be protected under all circumstances,” she added.
The Geneva-based organisation said tens of thousands of women, men and children had fled fighting in Duekoue since Monday.
The city lies on a strategic crossroads in the west of Ivory Coast and has been under the control of forces loyal to Mr Ouattara since Tuesday.
The International Organisation for Migration (IOM) said many Duekoue residents were heading to the nearby town of Guiglo “fearing for their lives”.
Gbagbo ‘going nowhere’
The national army has put up almost no resistance since Mr Ouattara’s supporters launched an offensive to oust Mr Gbagbo on Monday, sweeping down from the north to capture the capital, Yamoussoukro, and the key port of San Pedro.
However, they have been unable to defeat those still loyal to the former president in parts of Ivory Coast’s main city, Abidjan.
There have been fierce clashes outside the presidential palace and the headquarters of state television in the upmarket district of Cocody. Fighting has also been reported in Plateau and Agban areas.
While figures for dead and wounded are unavailable, Doctors Without Borders said it had treated at least 80 people over the past two days, most of them young men suffering from gunshot wounds.
Residents of Abidjan say they are afraid to leave their homes.
The BBC’s John James in Bouake says Mr Gbagbo is holed up inside the fortress-like presidential mansion, with his last remaining allies and the Republican Guard.
“Laurent Gbagbo is going nowhere. He is the elected president of Ivory Coast and he is going to be president for five years to come,” a spokesman for Mr Gbagbo’s Ivorian Popular Front (FPI) said.
Our correspondent says many wonder whether he has now decided to go down with the ship, a strongman who has brought West Africa’s second biggest economy to its knees in his determination to hang on to the presidency.
But Patrick Achi, a spokesman for Mr Ouattara, said there was no longer an offer on the table for Mr Gbagbo to stand down peacefully.
“He should stand trial in the International Criminal Court. That is the only thing that he deserves,” he added.
The international community stepped up its pressure on Mr Gbagbo with a series of calls for him to stand aside.
The West African bloc, Ecowas, urged Mr Gbagbo to “end the suffering of his country”, while the UN mission in Ivory Coast (UNOCI) said it was ready to “facilitate his departure if that is his wish”.
Western diplomats say it is impossible now for Mr Gbagbo to escape defeat, but it is unclear if he will come of this alive given the scale of the fighting around the presidential villa, our correspondent adds.
UN forces are patrolling Abidjan’s business district in armoured cars and flying helicopters to conduct surveillance. France has meanwhile announced it is increasing its force in Abidjan from about 900 troops to some 1,100.
A curfew called by Mr Ouattara from 2100 GMT to 0600 GMT in Abidjan remains in place. Land and sea borders remain closed, although on Friday the country’s air space was reopened.