Smoke rose from smouldering heaps of lava in the Buhene area near the city.
Ndima reported some thefts from shops and an attempted escape of inmates from Goma prison but said 'the situation is under control'.
Many families slept on pavements surrounded by their belongings under a night sky turned red by the eruption of Africa's most active volcano.
In addition to many homes, the lava destroyed several health centers, a primary school, a water pipeline and Goma's main electricity supply line, Muyaya said.
"We just had a big aftershock - I'm scared to stay in my office", said a resident who gave her name only as Deborah, an employee at an worldwide organisation, reached by telephone.
Pope Francis offered a special prayer for Goma during his weekly Angelus prayer at the Vatican Sunday, when the area felt around a dozen tremors.
One Goma resident, Richard Bahati, said he was in his house when he heard screaming and became extremely anxious as he saw the sky reddening outside.
Despite a relative return to calm Goma residents remained wary.
"There is a smell of sulphur".
"They're multiplying and they come at any moment", one resident told AFP, describing the aftershocks as "very worrying".
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Others, she highlighted, "Are elderly Congolese who are concerned that the volcano could still erupt at any given time during the day".
A Reuters reporter saw two people killed by the initial eruption in a village north of Goma, and witnesses spoke of dead and missing relatives.
A few cars were on seen on the streets, but no police or military presence was visible.
Fire and strong fumes emanated from the blackish molten rock as it swallowed up houses, heading towards Goma airport on the shores of Lake Kivu.
General Ndima said MONUSCO, the United Nations mission in the country, along with NGOs and worldwide organisations in the DRC, would hold an emergency meeting on Sunday with local and regional authorities. There was no official word on how many may have been killed amid the scramble to flee the city late Saturday.
Power was already cut in large parts of the city when hundreds of residents began leaving their homes.
Meanwhile, some 8,000 people crossed the country's border into Rwanda to seek refuge following the eruption, according to the Rwandan Ministry in Charge of Emergency Management, which said most people were returning home Sunday morning after the lava flow had stopped.
"When we returned to the city the houses were burnt and some people were left destitute".
The Observatory's Adalbert Muhindo said ongoing tremors meant people had to remain vigilant and warned it would be unsafe for locals who had fled to think of returning to the vicinity for now. But still, thousands evacuated - many across the border into Rwanda - remembering the widespread devastation that the last eruption in 2002 caused, when reports of the death toll ranged into the hundredsand tens of thousands of homes were lost. Current assessments indicate eruption doesn't threaten the city itself.