Authorities say many were killed the violence, which saw corpses burnt beyond recognition and bodies reportedly thrown into wells, but have refused to give a toll, saying it could spark reprisals and would be inaccurate.
There were reports of fresh clashes in the northern state of Kaduna overnight, with a community leader telling local radio "the killing was unbelievable and the destruction is colossal."
One government official, explaining authorities' reluctance to release an overall death toll from since the vote on Saturday, said, "I wouldn't like to use the term massacre... some places it was terrible."
Curfews and military patrols appeared to have brought an uneasy calm to many areas on Wednesday as the thousands who fled their homes in fear took refuge at police and military barracks, sleeping in the open under trees.
The Red Cross said it had counted around 410 people wounded in the violence that began sporadically in the country's mainly Muslim north before spreading to some 14 states on Monday.
It has also said there were many dead but has declined to give a number.
The number of displaced had increased to 39,700, its disaster management coordinator Umar Abdul Mairiga told AFP on Wednesday.
The Red Cross warned that slow arrival of aid to those displaced by the unrest was causing anger to build, but a spokesman for the national emergency management agency said help was being hurriedly organised.
Nigeria, Africa's most populous nation, is roughly divided in half between a mainly Muslim north and predominately Christian south.
The north, on the edge of the Sahara, has long been economically marginalised when compared to the oil-rich south, fuelling resentment and divisions that Saturday's elections helped expose.
Authorities have however argued that the rioting was not based on religion or ethnicity but was instigated by those unhappy with the victory of incumbent Goodluck Jonathan, a southern Christian.
Jonathan took over in May 2010 following the death of his predecessor Umaru Yar'Adua, a northern Muslim who had not finished his first term, prompting bitterness in the north over its loss of power.
In the most intense rioting on Monday, mobs roamed the streets with machetes and clubs, pulling people out of cars and setting homes on fire. Reprisal attacks intensified the situation.
In the main northern city of Kano, a Christian woman taking refuge at a police station said she had fled through back alleys with her three children after she saw smoke and heard shouting.
"We left our homes for fear of attacks from the mobs," said Mary Okechukwu, 36. "Many have gone back to their homes, but ... I will not risk my life and that of my children."
The main opposition presidential candidate, ex-military ruler Muhammadu Buhari, has alleged widespread irregularities in Saturday's election but urged calm and said he would pursue his complaints through legal means.
In some areas "our supporters weren't allowed to vote," the northerner told Voice of America radio's Hausa-language service.
Jonathan was declared the winner with 57 percent of the ballots, easily beating Buhari with 31 percent.
Amid the violence, Jonathan announced Tuesday he was suspending his interior minister.
While the rioting began over allegations that Jonathan's party had sought to rig the vote, the situation appeared more complex in some areas.
In remote parts of Kaduna state, residents alleged Christians had initiated the violence, leading to clashes police were unable to control.
There were also indications that Muslims were fleeing areas of the southeast in fear of reprisals and seeking refuge in military barracks, according to an official who spoke on condition of anonymity due to the sensitivity of the situation.
Despite the post-poll violence, observers have hailed the conduct of the vote as a major step forward for a nation with a history of violent and deeply flawed elections, while noting serious problems remained.
US Secretary of State Hillary Clinton congratulated Jonathan, saying the vote marked a "positive new beginning" for Africa's largest oil producer.
"This historic event marks a dramatic shift from decades of failed elections," she said, though cautioning that the process was "far from perfect."