Large number of troops and police were still out on the streets on Thursday morning, as the city emerged from a night-time curfew.
But people were seen going out to work for the first time since the trouble broke out on Monday and a number of businesses and markets have re-opened.
The Kaduna state governor, Ahmed Markafi, has been summoned for urgent talks about the violence with President Obasanjo.
Arrests
Police say they have arrested more than 100 people, including some wearing fake army uniforms.
Mobile courts have been set up to try people carrying arms illegally or violating the curfew imposed on Tuesday.
Hundreds of buildings were set on fire during the two days of clashes between Christians and Muslims.
Hospital sources told Reuters news agency that more than 200 people had died, while the head of a local inter-religious group, James Wuye, put the figure at 300.
The police, who are sticking to a figure of 43 deaths, are reported to have been ordered not to reveal the full toll for fear of sparking revenge killings.
Officials said that dozens of the victims, many burnt beyond recognition, were buried in a mass grave on Wednesday to take pressure off hospital mortuaries.
National implications
In a statement, the Nigerian government said it was profoundly touched by the tragic events in Kaduna.
President Obasanjo, who is a Christian, said that and his Muslim vice-president would work together to restore harmony.
The state governor, Ahmed Markafi, told the BBC that if anything were to go "massively wrong" in a political and security centre like Kaduna, "it is likely even to bring down the civilian government at the federal level".
For his part, Mr Markafi blamed rumours for aggravating the violence. He said rumours had even circulated that he himself had been killed, in order to heighten Muslim-Christian tension.
Police say the latest clashes broke out after residents of a mainly Christian neighbourhood blamed Muslims for the killing of a local man.
Three months ago, more than 1,000 people in Kaduna were killed in clashes over plans to implement Islamic law, or sharia, in some northern Nigerian states.