Sudan has rejected allegations that it is carrying out atrocities in its South Kordofan region.
Mukesh Kapila, of rights group Aegis Trust, said he had seen planes dropping bombs on villages and civilians running for shelter in caves.
The government said any crimes against humanity are being committed by rebels backed by South Sudan.
South Kordofan is one of three areas hit by conflict since South Sudan became independent from Sudan in July.
Abyei and Blue Nile along with South Kordofan lie along the loosely demarcated border between Sudan and South Sudan.
Rabie Abdul-Atti, an official with the government in Khartoum, accused South Sudan of sending troops into the area.
He said the Juba government was providing logistical support for rebels who support the newly independent South Sudan.
South Sudan has denied these claims.
Mukesh Kapila, who used to be the UN's most senior humanitarian official in Sudan, said he saw Sudanese planes bombing civilian areas in South Kordofan.
"We heard and saw the planes on top of us," he told the BBC after visiting the southern region of Sudan for the Aegis Trust, which campaigns against genocide.
"And then we saw women and children, who I had only just been talking to a few seconds before, run away to the caves and cracks in the hills where they traditionally took shelter when the bombers came in, which apparently happens every day."
Mr Kapila said similar tactics had been used in Sudan's Darfur region in the past.
"We saw water wells being targeted. We saw churches destroyed where people might take shelter from the fighting. And we saw, for the first time reported, the use of anti-personnel landmines and cluster bombs," he said.
The BBC's James Copnall in the capital Khartoum says the war in South Kordofan is getting increased attention, in part because of fears of lack of food in the rebel-held areas.
Khartoum is not allowing international humanitarian agencies into the area, and has been accused of using food as a weapon of war.
Khalid Al Mubarak, a spokesman for the Sudanese Embassy in London, told the BBC that it does allow in Sudanese aid agencies, but not agencies the government says are trying to work against stability in the area.
The UN has called for an end to cross-border violence, and has urged both countries to implement a non-aggression pact signed on 10 February.
There has been fighting in Darfur since 2003, while violence in South Kordofan broke out last year.