The rights group revealed new evidence of summary killings of supporters of strongman Laurent Gbagbo in the far west of the strife-torn country as Ouattara followers seized Gbagbo territory.
But it also detailed atrocities such as the killing of 100 men, women and children in a northern town by Gbagbo's fighters and other deadly attacks in nearby towns and villages.
Ouattara denied to UN leader Ban Ki-moon that his forces were involved when Ban asked him about the killings last week. The UN Security Council is to discuss the massacres this week, even as the crisis draws closer to an end with Gbagbo now surrounded in his bunker in Abidjan.
"To understand the tragic events in Ivory Coast, a line cannot be drawn between north and south, or supporters of Gbagbo and Ouattara," said Daniel Bekele, HRW's Africa director.
"Unfortunately, there are those on both sides who have shown little regard for the dignity of human life."
The international Red Cross has already said up to 800 people were killed in a massacre in the western town of Duekoue in late March.
According to the United Nations, about 230 bodies have been found in Duekoue so far and another 100 in other towns and villages. It says Ouattara has agreed to hold an investigation.
HRW reinforced the Duekoue accusations against the followers of Ouattara, who was declared by the UN as winner of a presidential election in November, and brought new accounts of atrocities in other towns and villages.
It said hundreds were killed in Duekoue after the town was secured on the morning of March 29.
"Fighters from the Republican Forces -- accompanied by two pro-Ouattara militia groups -- proceeded to the Gbagbo-stronghold neighborhood of Carrefour.
"Eight women told Human Rights Watch that pro-Ouattara forces dragged men, young and old, out of their homes and executed them with machetes and guns in the street, sometimes with multiple rounds of bullets."
HRW said it interviewed more than 120 witnesses of killings and relatives of victims on the Liberia-Ivory Coast frontier and contacted 20 others in the western towns of Guiglo, Duekoue, and Blolequin by telephone.
The group accused the Republican Forces of Ivory Coast, which is controlled by Ouattara's Prime Minister, Guillaume Soro, of killing opponents between March 6 and March 30 as they took territory from Gbagbo's forces.
Many of those killed were ethnic Guere who mainly supported Gbagbo in last year's election.
Many elderly Ivorians were killed because they were too infirm to flee to Liberia.
Dozens of women were repeatedly raped, said the report. One woman from Bakoubli, near Toulepleu, said the forces raped her in front of her children, then killed her husband who tried to intervene.
It quoted one 47-year-old woman as saying she was forced to watch as her father, husband, and 10-year-old son were killed around the family's cocoa farm near Doke.
A 32-year-old man described pro-Ouattara forces entering the town of Diboke and opening fire on civilians as they ran out to see which side had entered.
HRW said it found evidence of atrocities by Gbagbo forces, including the March 28 massacre in Blolequin of more than 100 men, women, and children from northern Ivory Coast and neighboring West African countries. One day later another 10 northerners and West African migrants were killed in Guiglo while eight Togolese were slaughtered in a village just outside Blolequin.