More than 300,000 people across Sudan have been affected by floods which killed almost 50 people this month, the UN's World Health Organisation said in a statement received Thursday.

The data came as a new thunderstorm and strong winds on Thursday night rattled the Khartoum region, already suffering from what the UN said was the worst inundation in 25 years.

"Heavy rains and floods in Sudan have affected lives and properties of some 65,957 families or 320,000 people," WHO said in a report.

As of Wednesday, 48 people had been killed and 70 injured, while property damage has been reported in 14 of the country's 18 states, WHO said.

Interior Minister Ibrahim Mahmoud Hamed gave a higher death toll of 53 last week.

The WHO said one of the major health concerns was the collapse of almost 53,000 latrines.

In addition to damage from the flash floods which struck urban neighbourhoods earlier this month, the Blue Nile river in Khartoum has risen.

AFP reporters on Thursday saw the river had washed over about one kilometre (half a mile) of farmland in the east of the city, but a sand berm appeared to have been erected in an effort to block further intrusion.

"This is a huge disaster," Mark Cutts, who heads the UN's Office for the Coordination of Humanitarian Affairs in Sudan, said last week.

He said the UN is ready to support the government to help those affected by the floods, even though UN humanitarian operations in Sudan "have been severely underfunded" in 2013.

Aid workers were also assisting hundreds of thousands displaced this year by worsening fighting in the western Darfur region.

More than one million more have been uprooted or severely affected by war in South Kordofan and Blue Nile.

Foreign aid to assist flood victims has flown in from Morocco, Qatar, Ethiopia and Egypt, according to official media.