Sudan's cabinet met in emergency session on Tuesday after flooding killed 39 people, destroyed thousands of homes and sparked complaints of government negligence.

Interior Minister Ismat Abdul-Rahman told the meeting that "39 people died across the country, 17 of them from Khartoum state," the official SUNA news agency said.

"Most of the country has been affected by above-normal heavy rain," he reported, detailing a total of almost 5,500 collapsed houses in five states early in the rainy season.

Most of the damage was in the Khartoum region, his figures showed.

The downpours have led to a noticeable rise in the Blue Nile River in Khartoum, and Water Resources Minister Muattaz Musa Abdallah Salim told the cabinet meeting that higher river levels "may cause more floods", SUNA reported.

As Sudan's rainy season begins, there have already been three brief, violent storms in the capital region and beyond since July 25.

After the latest ferocious downpour early Sunday, AFP found hundreds of families living among the rubble of their collapsed homes in the Salha district of Khartoum's twin city Omdurman.

They complained that emergency shelter and other help has been slow to arrive but Khartoum state Governor Abdel Rahman al-Khidir said "all affected families" had received tents and other aid by Monday.

The opposition Reform Now party has called for Khidir's dismissal "because he completely failed to have a solution to the rainy crisis which is repeated every year."

Khidir, however, said there is a flood-prevention plan.

Among the measures, Khartoum is building a 2,200-kilometre (1,364-mile) concrete drainage system under a seven-year project, he said, according to SUNA.

After flooding last year, AFP observed a drainage canal under construction beside a road near the Blue Nile but months later the work remained incomplete.

Sudan Change Now, an activist youth movement, has blamed "the government's corruption" for flooding.

State authorities are pumping out rain water from flooded open areas of the capital region, Khidir said.

Water tankers have been seen working on the city's muddy streets.

An inundation last August was the worst to strike the capital in a quarter-century and affected more than 180,000 people, the United Nations said.

Those floods caused about 50 deaths nationwide, most of them in Khartoum.