Lambert Mende said the epicenter of the earthquake was located close to Lake Tanganyika near Bukavu, the capital of the South Kivu province.
He said a house collapsed in Katana, near the airport in Bukavu, causing the death of the children. He further said the earthquake also caused some cracks in buildings.
Mende said the earthquake could also be felt in Goma, the capital of the North Kivu province which is about 217 kilometers (135 miles) by land on the north end of Lake Kivu, AP reported.
Eastern Congo has been mired in violence since the aftermath of the 1994 genocide in neighboring Rwanda.