Crude camps housing South Sudanese have been flooded by heavy rains that inundated the Sudanese capital over the Eid al-Fitr holiday, a southern diplomat said on Wednesday.

Rain and high winds lashed Khartoum overnight Tuesday, soaking homes and streets for the second time since Friday at the start of the rainy season.

There were no reports of casualties but Kau Nak, charge d'affaires at the South Sudanese embassy, said many of his country's nationals in ramshackle settlements known as "open areas" have been affected.

"Most of the open areas are flooded and there's nowhere to go," Kau Nak told AFP, adding that he planned to assess the damage on Thursday.

The thousands of impoverished open-area residents include some who fled north after civil war began last December in South Sudan.

But many others have been in the squatter settlements for much longer, having gathered there in the vain hope of getting assistance to travel South after the country's independence three years ago.

A survey by the International Organisation for Migration (IOM) in late 2013 found almost 20,000 people in the open areas.

More than 86,000 South Sudanese have fled to Sudan, mostly to White Nile state, since war began there in December, according to the United Nations.

Some have made it as far as Khartoum, joining those who have been there longer in their rough outdoor settlements.

About 160 houses in the Khartoum region have been totally or partly destroyed after the latest violent downpour, according to a preliminary assessment cited by the official SUNA news agency on Wednesday.

Khartoum governor Abdel Rahman Al-Khidir said schools would stay closed for holidays one week longer than planned, until August 10, "due to the current rains and flooding situation", SUNA said.

More rain is forecast.

Flooding in the Khartoum area last year affected more than 180,000 people and was the worst in 25 years, according to the UN.

The government said about 50 people died. Most of those deaths were in the capital.