Heavy rains usually fall in Sudan from June to October, and the country faces severe flooding every year.
But this year officials said they had recorded the highest waters on the Blue Nile -- which joins the White Nile in the Sudanese capital Khartoum -- since records began over a century ago.
On September 7 the waters had reached 17.67 metres (58 foot), but by Sunday the level went down to 17.36, the ministry said, adding that the drop was being registered in several control stations across the country.
On Thursday the UN said that the floods had affected more than half a million people in Sudan, destroyed or damaged tens of thousands of homes and raised the risk of water-borne disease outbreaks.
According to Sudan's civil defence, at least 106 people have been killed and 54 others injured.
The disaster prompted the Sudanese government to declare a three-month state of emergency.
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