Sudanese President Omar al-Bashir on Thursday reshuffled senior military officers after his troops carried out intense operations against rebels across war-torn regions, including in Darfur.

The changes -- the second such within six months -- follow a flare-up of deadly violence in neighbouring South Sudan, which split from the north five years ago.

Bashir declared in June a four-month ceasefire in the states of Blue Nile and South Kordofan, where recent fighting between troops and rebels left scores of casualties.

His troops continue to fight rebels in Darfur's mountainous area of Jebel Marra, although Khartoum says the overall unrest in Darfur has ended.

On Thursday, Bashir issued a decree appointing new minister of state for defence, new army intelligence chief, new commander for infantry and new chief of joint operation.

Ali Mohamed Salim has been named as the new minister of state for defence, the army said in a statement late Thursday.

Salim, who was the army intelligence chief, takes over from Ibrahim Al-Hassan, who in turn replaces Salim as the army intelligence chief.

Bashir also named Naser Awad al-Kareem as the new chief of joint operation and Elsier Bashir as the new chief of infantry.

In Blue Nile and South Kordofan, Bashir's forces have been battling the rebel Sudan People's Liberation Movement - North (SPLM-N) since 2011.

Neither side has decisively gained an upper hand in the fighting in the two states.

The ceasefire does not extend to Darfur as Khartoum says "there was no rebellion now" in the region.

Sudan held a referendum in Darfur in April, with officials saying almost 98 percent of voters opted for retaining the region as five separate states.

Darfur has been gripped by conflict since 2003, when ethnic minority rebels rose up against the government in Khartoum, following which Bashir launched a counter-insurgency in the region.

At least 300,000 people have been killed in Darfur, the United Nations says. Another 2.5 million have fled their homes.

Bashir himself is wanted by the International Criminal Court on war crimes charges related to Darfur, which he denies.

Meanwhile in South Sudan, hundreds have died in the latest round of violence that broke out in the capital ahead of the country's independence anniversary last week.

South Sudan voted for independence from Sudan under a peace agreement in 2011, but the world's newest country fell into a civil war that has killed tens of thousands of people.

Although a ceasefire has held since late Monday, the United Nations has warned of tension and the possibility of fresh fighting in Juba.

Specially chartered evacuation flights have been taking foreign nationals out of the country since Wednesday.