Those removed by President Salva Kiir include two of the country's most influential leaders – his rival vice-president Riek Machar and Pagan Amum, secretary-general of the ruling party, the Sudan People's Liberation Movement (SPLM).
The sackings have sparked concern over potential instability in the fledgling nation, awash with guns, riven by ethnic rivalries and still reeling from decades of war.
"We are asking our citizens, please do your duty and go to work," said Barnaba Marial Benjamin, who until his suspension late on Tuesday was the information minister and government spokesperson.
All 29 ministers were suspended as well as their deputies, in addition to 17 police brigadiers.
"Give the president a chance to form his government … he has already empowered the technocrats to see the day-to-day running of the administration," Benjamin said in a broadcast on the United Nations-supported Radio Miraya.
Troops and armed police blocked several key roads in Juba, with a heavy deployment at the government ministry complex, but the city was reported calm, army spokesperson Philip Aguer said.
"This is routine work, they are being deployed to protect the ministries," Aguer told Agence France-Presse.
Rebel figures
Many of the ministers were key figures in the rebel SPLM or its armed wing that fought a brutal 1983-2005 war against the government in Khartoum, which led to a 2011 referendum in which South Sudan voted overwhelmingly to split from the north.
Machar, from the Dok Nuer people from the key oil producing Unity state, is a controversial figure for many, but commands loyalty among many branches of the Nuer, which form an integral part of the footsoldiers of the new nation's ex-rebel army.
He has made no secret of his desire to challenge Kiir for the presidency in elections due in 2015.
However, he fought on both sides of the civil war, leading a splinter SPLM faction that sided with Khartoum, battling troops commanded by Kiir, who comes from the Dinka people.
Machar's troops are accused of a brutal massacre in the ethnic Dinka town of Bor in 1991.
Mismanagement
​Amum was the top negotiator with arch-foes Sudan at long-running African Union-mediated talks over a raft of issues left unresolved at independence, including border demarcation and oil exports, currently under threat of suspension again, this time by Khartoum.
The suspended party leader is to be also investigated for alleged "mismanagement of the party" by a parliamentary committee, the presidential orders broadcast on state radio said.
No replacements have been announced, and it was not immediately clear whether all those suspended would return, or if new blood would be brought in to replace them.
While Juba has been rife with rumours in recent weeks about a potential reshuffle by Kiir – especially concerning tense relations with his deputy Machar – the move still took those involved by surprise. – AFP