The UN statement said investigators "visited 11 communal grave sites, containing at least 26 bodies, fighters and civilians".
Nkunda, who was not invited to the talks in the Kenyan capital, has issued a "categorical denial" that his fighters were behind any civilian deaths in Kiwanja.
Human Rights Watch says at least 100 civilians have been killed and more than 200 other wounded since the fighting resumed in late August.
Moses Wetangula, Kenya's foreign minister, reading a communique agreed by seven African leaders, said: "There should be an immediate ceasefire by all the armed men and militia in North Kivu."
He said that regional peacekeepers could be sent to North Kivu if required.
The meeting also called for the establishment of a "humanitarian corridor" to aid the tens of thousands of refugees displaced by the fighting.
Al Jazeera's Zeina Awad, reporting from Nairobi, said: "They have told us they've put forward a mechanism ... that will shuttle between all the parties, including Laurent Nkunda.
"He was not at the table today, but talking to him has not been ruled out."
Babou Amane, deputy spokesman for Nkunda's forces, told Al Jazeera: "The African summit is following us in our decision to have a unilateral ceasefire ... we would like the summit to force the [Congolese] government to follow up the ceasefire.
"We have asked the government to sit round the table so we can discuss our issues ... [but] if the government engages us, we will respond," he said.
There are fears that regional forces could be drawn into the conflict and Ban Ki-moon, the UN secretary-general, warned delegates at the Kenya summit that the conflict could grow to engulf the region.
"It is only at the political level, here in your region, that lasting solutions can be found. There can be no military solution to this crisis," he said.
Ban denied an earlier UN report saying that Angolan troops had joined Congolese soldiers battling rebels near Goma.
On Friday, a UN official and a Uruguayan peacekeeping officer said that an unspecified number of Angolan troops arrived four days ago. The two officials spoke on condition of anonymity.
In New York, Edmond Mulet, the UN assistant secretary-general for peacekeeping, suggested some people may have mistaken Congolese government troops who had trained in Angola, and therefore spoke Portuguese, for Angolan troops.
There is widespread concern that the involvement of Angolans could spread the conflict beyond Congo's borders. The war in Congo from 1998 to 2002 drew in more than half a dozen African nations.
The DR Congo government has repeatedly said that Nkunda's forces are backed by Rwanda's Tutsi administration.
During the talks, clashes continued between Nkunda's fighters and Congolese government forces close to the Kibati refugee camp, where there are about 45,000 refugees from the fighting elsewhere in North Kivu province.
"The fighting is getting more intense here," Al Jazeera's Mohammed Adow, reporting from Kibati refugee camp, said, adding that he could hear heavy artillery fire near the camp.
"And this fighting is taking place less than 7km from Goma."
The UN's refugee agency said that the shooting lasted for about 30 minutes, causing panic among the refugee population and interrupting aid distribution.
The road south towards Goma was again lined with refugees fleeing the conflict, as it had been last week.
The French aid group Doctors Without Borders reported that fighting had also taken place in the towns of Rutshuru and Kiwanja, forcing staff sent to the area to turn back.
The UN estimates that about 253,000 people have been displaced since September.