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9 March 2012 Last updated at 05:22 ET
Col Abdildem Dafalla said he had between 8,000 and 9,000 men fighting across the border in Blue Nile
Rebel alliance
Rebel ammunition in border area waiting to be walked up to front line positions
Supplies are now arriving in South Sudan's refugee camps, but not in conflict zones across the border
Sudan's hidden conflict: Rebels, raids and refugees
Largely hidden from the world's media, a conflict is raging in the border area between Sudan and the new nation of South Sudan. The BBC's Martin Plaut reports from the border on the plight of the thousands who have fled their homes and the rebels' motives.
"I clutched my children to my bosom, when the Antonov bombers came," says one grandmother, who crossed into South South with her 29 children and grandchildren.
We cannot name her, since she hopes one day to go home.
A scattering of refugee camps along the borders have been erected by the UN refugee agency (UNHCR) to serve their needs.
Just one - Jammam refugee camp, in Maban county of Upper Nile state - is home to some 34,000 people.
Col Abdildem Dafalla said he had between 8,000 and 9,000 men fighting across the border in Blue NileIt is estimated that around 100,000 people have fled their homes since the second half of 2011, when the Sudanese government launched an offensive against rebels in Blue Nile and South Kordofan, in the south of Sudan.
Most set off with nothing but the clothes they wore.
Families we spoke to say many of their children and elderly were too weak to make the journey, and died along the way.
First estimates of the scale of the crisis by aid agencies proved inadequate, and the United Nations had to rapidly increase the scale of its operations.
Now a route has been opened through the port of Djibouti and on through Ethiopia and into South Sudan.
It is a journey of six to seven days, but the trucks towing trailers of basic supplies are now arriving to feed these huge camps.
The rebels who are taking on the government in Khartoum are the Sudan People's Liberation Movement-North (SPLM-North).
They see themselves as continuing in the footsteps of the movement from which they sprang, the SPLM of the late John Garang, which now runs the newly independent state of South Sudan.
When independence came in July last year, many SPLM forces in Blue Nile and South Kordofan were left stranded in Sudan.
These areas were supposed to have been allowed a vote to choose autonomy, but this was blocked by Khartoum.
Neroun Philip Aju, the SPLM-North's humanitarian co-ordinator in Juba, the capital of South Sudan, says the aim is to change the government in Khartoum - not to form another new state.
Fighting is vicious, with refugee after refugee explaining how they have been bombed from the air, with markets being a particular target.
This is likely to intensify as the SPLM-North has concluded an agreement to link up with three rebel movements fighting in Darfur.
A conflict that brings together South Sudan and the west of Sudan could prove a real headache for the authorities in Khartoum.
Until now the SPLM-North has been a somewhat unknown quantity. There are few hard facts about its operations in Blue Nile state and no independent sources of information.
Rebel ammunition in border area waiting to be walked up to front line positionsBut visiting the border area in Maban County, South Sudan, we pieced together a picture of the movement.
We saw no training bases or rebel camps.
This is a military zone and there were plenty of men in uniform from the South Sudan government forces - the rebels we did meet were in civilian clothes.
In a border village, we ran into Col Abdildem Dafalla of the SPLM-North, who told us he has between 8,000 and 9,000 men fighting in Blue Nile.
"We are moving around. If a specific place is attacked, we move away and then return to it when the Sudan government forces have left."
Asked whether his forces could win, he was confident: "100%, we'll win."
"We have not even requested support or ammunition from any other country because we know we can win this fight," he said.
The SPLM-North routinely denies receiving support from South Sudan, and the government denies any connection with the rebels.
Juba signed an agreement with Khartoum not to support rebellions in each other's states, but there are strong suggestions that both sides flout this pact.
Help from outsideDaily life for people in the Sudanese states of Blue Nile and South Kordofan is reported to be dire, with hundreds of thousands of displaced - many living in caves in the hills to avoid aerial bombing which happens day and night.
Supplies are now arriving in South Sudan's refugee camps, but not in conflict zones across the borderFormer UN official, Mukesh Kapila, who has just visited the area, told the BBC it reminded him of the "terror tactics" he had seen in Darfur.
"We saw whole tracts of deserted countryside and smoke rising from fires where fields of seeds that had been planted had been burnt off, " he said.
"We saw churches destroyed where people had run to take shelter. And we saw fear, hurt and anger in the eyes of the people we met."
Mr Aju showed the BBC a document signed by the UN, the African Union and Arab League calling for international aid to be allowed to flow directly into these areas of conflict.
"We have accepted that proposal for the delivery of aid to the affected population and we are waiting for the Sudan government to do the same," he says.
"March is a deadline. If nothing is done we will have a humanitarian disaster in South Kordofan and Blue Nile.
"If the Sudan government does not accept the proposal, we would ask the international community to put the food in anyway."
This might mean sending aid in without government approval - something the UN appears to be considering.
This could put the aid agencies in an extremely awkward position, caught between serving the needs of the people and the demands of the states in which they are operating.
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