A police statement said the explosions, which lasted an hour and a half on Wednesday, destroyed a market west of the town and damaged several homes and offices.
The official Sudan News Agency (SUNA), quoted a statement released by armed forces spokesman, Gen Al-Abbas Abdel Rahman al-Khalifa, as saying a warehouse where the ammunition was being kept blew up, causing a series of explosions and scattering live fragments. He said seven people were killed and 13 injured.
Khalifa, however, ruled out the possibility of "any hostile act behind the incident", saying the extreme temperature of the late-morning heat had caused the blast.
Other news sources, however, put the death toll much higher. The Sudan News Service reported that the death toll had risen up to 80 people, with about 250 injured.
Juba, southern Sudan’s largest town, has a population of about 160,000, and was controlled by Khartoum for the duration of the lengthy war between the north and south. The war ended in January.
Meanwhile the UN has said more than US $1 billion would be needed to fund the first year of the proposed UN peacekeeping mission in southern Sudan.
The proposed mission would have the mandate of helping the vast region stabilise and lay the groundwork for development after more than two decades of civil war.
In an addendum to his earlier report to the Security Council on the proposed mission, the UN Secretary-General Kofi Annan said the UN had projected that $147.5 million in one-off, start-up costs and $862.3 million in recurring costs would be required for the first 12 months of the mission's mandate, the UN News Service reported on Thursday.
"It is my recommendation that, should the Security Council decide to deploy the peacekeeping operation in the Sudan, the General Assembly consider the related costs as an expense of the organisation to be borne by member states - and that the assessments levied on member states be credited to a special account established for that purpose," Annan said in his report.
The costs are based on the deployment of 10,130 military personnel (including 5,070 troops), 755 civilian police officers, 1,018 international staff, 2,263 Sudanese staff and 214 UN Volunteers.
According to the report, the mission could face daunting logistical challenges in its efforts to reconstruct the southern region of Africa's largest country.
Apart from security problems, southern Sudan is extremely isolated, with "poor communications, few hardened roads or runways and an inoperable railway system", the report said. Transport problems could get worse during the rainy season while landmines and unexploded ordnance presented another risk, it added.
Annan's report follows the signing of the peace deal in January that ended the 21-year civil war in the south between the Sudanese government and the rebel Sudan People's Liberation Movement/Army (SPLM/A).
The agreement provides for power-sharing, some autonomy for the south and more equitable distribution of economic resources, including oil. A six-year transition period is to be followed by a referendum on whether southern Sudan should become an independent entity.