Around 20 people have been killed and dozens wounded in dawn attacks on a sit-in outside Sudan's defence ministry by protesters calling for President Omar al-Bashir to step down, the head of the main opposition party said on Tuesday.

Veteran leader Sadiq al-Mahdi also called in a statement for "a select military command" to negotiate a transition towards democracy, following more than three months of protests that represent the most sustained challenge to Bashir's 30-year rule.

Mahdi's remarks came as several thousand protesters continued for a fourth day a sit-in outside the compound in central Khartoum housing the defence ministry, Bashir's residence and the country's security headquarters.

Early on Tuesday, Sudan's National Intelligence and Security Service tried twice to disperse the protesters, breaking into the area using pickup trucks, witnesses said.

Security forces also tried to disperse the sit-in early on Monday, but witnesses and activists said soldiers moved to protect the protesters.

An opposition doctors' committee put the death toll in Sudan since the sit-in began on Saturday at 21, including five soldiers, with more than 150 injured.

Amnesty International said in a statement that nine people had reportedly been killed in Sudan since Saturday, and it had verified two deaths on Tuesday, one of them outside the compound.

The interior ministry could not immediately be reached for comment.

A senior leader of the Sudanese Professionals' Association (SPA), the main anti-government protest organiser, called on Tuesday for the sit-in to continue and for similar protests "in front of all armed forces headquarters throughout Sudan".

In the first public comments by a senior SPA leader, Omar Saleh Sennar also said his group wanted a civilian transitional government and would only negotiate with the army, considering it "the guarantor of the political system in Sudan".

"I am now, from the leadership of the Professionals' Association, present at the sit-in and more leaders of the association will subsequently appear to the public," he told Reuters by phone.

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