According to a spokesman for the regional administration, the first fighting in a provincial capital since rebels and the government signed a ceasefire in January.
Philip Jiben told Reuters that rebels loyal to the country's former vice president, Riek Machar, struck at around 7am and that SPLA government forces were engaged in battles in Malakal's northern, southern and central zones.
Rebel forces could not immediately be reached for comment, but President Salva Kiir's government and rebels who support Machar have both accused the other of violating the January 23 ceasefire deal brokered by neighbouring east African states.
The clashes will fuel concerns over the security of South Sudan's northern oil fields - an economic lifeline for the world's newest state - and raise pressure on both camps to revive stalled peace talks in neighbouring Ethiopia.
"The fighting is continuing, but our forces are still in control of Malakal," Philip Jiben, spokesman for the Upper Nile administration, told Reuters by telephone. Gunfire could be heard in the background as he spoke.
A UN official said he had received reports of fighting in Malakal but could not confirm them. The town fell into rebel hands after fighting first broke out in mid-December before the army recaptured it last month.
It was not immediately clear which rebel faction had attacked Malakal, a dusty market town on the banks of the White Nile. Machar says he controls all anti-government forces but analysts question the loyalty of some groups which have their own grievances against the Juba government.
STALLED PEACE TALKS
Thousands of people have been killed and more than 800,000 have fled their homes since fighting was triggered by a power struggle between President Kiir and Machar, his former deputy whom he sacked in July.
The conflict has already forced South Sudan to cut oil production by a fifth to 200,000 barrels per day, all of which is currently pumped from Upper Nile. Oil accounts for 98 percent of government revenues.
Oil firms in South Sudan, a country the size of France, include China National Petroleum Corp, India's ONGC Videsh and Malaysia's Petronas. Work in some fields has been suspended.
Peace talks had been due to resume last week, but were held up by a rebel demand that four remaining political prisoners held by the government be released and the Ugandan military, which is supporting Kiir's army, withdraw from South Sudan.
Government officials privately acknowledge negotiations are unlikely to make progress until the senior political figures are freed. The government accuses the detainees of an attempted coup.