Sudan's northern government has taken $6.51 million from the south's oil revenues, saying it was for custom exemptions granted to vital aid to rebuild the war-torn region, a southern official said.

The semi-autonomous southern government, created after a north-south 2005 peace deal, had granted customs exemptions for medicine, food, school supplies, emergency equipment and other materials needed for development and aid for the past two years.

"It doesn't make sense to impose custom duties on such imports as donor funded and for humanitarian services," Aggrey Tisa, acting undersecretary for the southern Finance Ministry, told Reuters on Wednesday.

He said the timing of the move as flooding continues to affect hundreds of thousands of southerners was bad. There was no immediate comment available from the government. Khartoum gives the south oil revenues monthly and Tisa said the customs money was subtracted from July's payment.

"They have subtracted a sum of $6.51 million as being the value of such exempted imports," Tisa told Reuters, adding it was unclear how exactly the sum had been calculated.

Under the 2005 peace deal the national government in Khartoum is to control all of Sudan's international custom tax.

Sudan makes millions of dollars from customs, visas and other fees levied on the world's largest humanitarian operation in Darfur and a massive post-war development effort in south Sudan.

Tisa said Khartoum maintained the exemptions were a violation of the peace deal, which also granted the south 50 percent of revenues generated from southern oil fields.

Tisa said his government wanted to reclaim the subtracted money and was in dialogue with Khartoum officials on how to find a solution to the problem.

He added his office had almost stopped issuing exemptions.

Under the deal the southern government should receive half the customs revenues generated in the south, but Tisa said they only received their first payment in July.

"We have not received our 50 percent. (But) they have agreed to provide our share a substantial figure," he said.