Goma-based volcanologist Dario Tedesco initially told Reuters news agency that the city did not appear to be at risk, but later Saturday a second fracture opened in the volcano, allowing lava to flow towards Goma.
"The situation is deteriorating", an official from Virunga National Park, where the volcano is located, told his staff in a memo.
The evacuation plan for Goma has been activated, said government spokesman Patrick Muyaya.
The government ordered an evacuation after the volcano, which overlooks the regional capital city Goma, began erupting Saturday.
"Besides the lava flow in the north east (Kibumba / Rwanda), the flow is also descending on the town".
Residents reported the smell of sulphur in the air and watched as the sky turned red.
The volcano last erupted in 2002, with some 250 people losing their lives and lava destroying approximately one-fifth of city, including airport runways.
Congolese President Felix Tshisekedi said he would be returning home on Sunday from Europe earlier than planned in order to help coordinate relief efforts.
Goma sits along the border between Congo and neighbouring Rwanda, and is a regional hub for many humanitarian agencies in the region, as well as the United Nations peacekeeping mission known as MONUSCO.
The Rwanda Broadcast Agency tweeted photos of those arriving in Rubavu district, adding they would be "accommodated in schools and places of worship that have been made ready". "I think that the lava is going towards the city centre".
On Saturday the Observatory was monitoring the direction of the lava flow, and said that for the moment it was heading towards Rwanda.
Thousands of Goma residents have fled the city on foot to reach the border with Rwanda as the city with a population of almost 2 million was illuminated with orange flames.
Others fled to Mount Goma, the highest point in the metropolitan area.
- The dark evening sky shines with hot red skin, says an AFP correspondent in Goma.
People tried to douse the flames as the lava flowed, engulfing parts of the city and roads.
Volcano watchers fear that the volcanic activity observed in the past five years will be similar to the years prior to the 1977 and 2002 eruptions. However, the observatory has been struggling to maintain its operations after the World Bank pulled funding over embezzlement claims.
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