By Hereward Holland

JUBA (Reuters) - Aerial bombardment and ground attacks by government forces in Sudan's restive south are targeting civilians as well as armed rebels and may amount to war crimes, a former senior United Nations official said.

Mukesh Kapila was the U.N. head of mission in Sudan in 2003, when rebels in the country's western Darfur region took up arms against the central government. The government mobilized troops and allied militias there to put down the revolt.

Hundreds of thousands died in the ensuing conflict, many of them civilians caught in the fighting or struck down by disease.

Returning to Sudan this month, Kapila said he went on a ten-day tour of rebel-held areas in South Kordofan and Blue Nile border states and found evidence of abuses that amounted to systematic ethnic cleansing.

"What's happened over the last two odd years ... is basically exactly the same tactics as Darfur except in the interim period the technology of war has improved," Kapila told Reuters in an interview.

Sudan's government insists its forces have committed no war crimes but says the rebels have sown chaos in South Kordofan and Blue Nile and are guilty of grave abuses.

Asked to comment on Kapila's findings, Rabie Abdelatie, a senior member of the ruling National Congress Party in Khartoum, said they were "completely incorrect".

"The government's responsibility is to protect civilians," said Abdelatie.

Armed revolts broke out in South Kordofan and Blue Nile around the time neighboring South Sudan declared independence in 2011.

On his 1,000 km (620 mile) tour of the southern regions, Kapila said he saw burned villages and bomb craters far from any fighting. He said government bombing had struck a blow to farming, causing severe food shortages, and hundreds of thousands of civilians had been displaced.

Sudan's government has banned aid deliveries even though it signed an agreement on the aid with the U.N. and the rebels in August. Khartoum said it needed assurances that aid could be delivered before giving the go-ahead.

Kapila said 2.5 million people now had limited or no access to humanitarian assistance.

"This is the world's biggest human rights disaster," said Kapila, who now works as a special representative for the Aegis Trust, an organization that campaigns to prevent genocide. "The tactics they are using point towards war crimes and crimes against humanity being committed with the circumstantial evidence that it is quite strongly ethnically based."

SANCTIONS

He urged the international community to use diplomatic isolation and economic sanctions to push Sudan to allow humanitarian access to the rebel-controlled border areas.

Kapila, whose assignment as U.N. envoy ended in 2004, was speaking in the capital of South Sudan, which split away from Khartoum under the terms of the peace deal that ended the two-decade conflict.

The rebels in South Kordofan and Blue Nile - known as the SPLM-North - fought as part of the southern insurgent army during a civil war in Sudan that lasted from 1983 to 2005.

Sudan now accuses South Sudan's government of supporting the rebels in the border states.

The government in Juba strongly denies that, saying it severed links with the insurgents when it gained independence, but the issue continues to strain relations between the nations.

In Darfur, violence flared again at the end of December. More than 100,000 fled some of the worst clashes there between government troops, rebels and rival tribes in months, the U.N. said.

The International Criminal Court has issued arrest warrants for Sudan's President Omar Hassan al-Bashir and other senior officials on charges of masterminding genocide and war crimes in Darfur.

They deny this and refuse to recognize the court. Khartoum puts the death toll from the Darfur conflict at 10,000.

Kapila warned the violence in South Kordofan and Blue Nile could reach a similar scale as Darfur and said the crimes being committed in those states needed to be investigated.

"There's more than enough prima facie evidence that a properly constituted inquiry should determine the nature of these crimes, and I can't understand why that's not happening," he said.

(Editing by Tom Pfeiffer)