The full horror of the campaign of violence that the government in Khartoum has unleashed against the black African Nuba people of Sudan has been laid bare in two confidential reports by the UN peacekeeping force that the Observer has obtained.

The accounts of "devastating" daily aerial bombardment of civilians, "indiscriminate shelling" of crowded civilian areas, summary executions and deliberate targeting of dark-skinned people are contained in a 19-page report requested by the UN security council. A second report details how "active obstruction by state authorities (in South Kordofan) has completely undermined the ability of the peacekeeping force, UN Mission in Sudan (Unmis), to fulfil the most basic requirements of its mandate" in the Nuba region.

The report says the humanitarian assistance and protection provided by Unmis have become "inconsequential" as it prepares to leave Sudan, at Khartoum's insistence, by 31 July. Unmis officials say privately that they have been "deaf and blind" in South Kordofan ever since war broke out on 5 June and cannot even estimate how many people have been killed and displaced by the fighting – widely perceived as a first step towards President Omar al-Bashir's stated goal of suppressing ethnic and cultural diversity in favour of a rigid Arab-Islamic regime, following South Sudan's decision to separate from the North.

The UN undersecretary-general for humanitarian affairs, Valerie Amos, said on Friday that 1.4 million people were affected by what she called "skirmishes" in South Kordofan, which borders the now independent Republic of South Sudan, and by Khartoum's refusal to grant "unhindered access" to them. Causing fury among hard-pressed colleagues on the ground, who have been crying out for much stronger support from the security council, she appeared to cast doubt on their reporting, saying: "We do not know whether there is any truth to the grave allegations of extra-judicial killings, mass graves and other violations in South Kordofan."

The Nuba Sudan People's Liberation Movement/Army (SPLM/A) – formerly allied with the South, but now seeking a northern alliance to overthrow the Bashir government – claims that more than 400,000 people have been displaced and 3,000 killed or disappeared. One Unmis staffer, quoted in one of the documents seen by the Observer, reported seeing the bodies of approximately 150 Nuba lying in pools of blood in just one of the many army barracks in the state capital, Kadugli.

Khartoum and the SPLA have accused each other of starting the fighting, after a ceasefire that began in 2002. Unmis's report for the security council, prepared by its human rights section, notes that the SPLM/A refused to accept the results of disputed state elections in May, but says there is no evidence that it initiated military operations. Rather, it says, the fighting may have been triggered by an ultimatum for Nuba fighters to move to South Sudan by 1 June – an order that was tantamount to "disenfranchising them of their citizenship", given the promise of partition in July.

The report suggests that the "especially egregious" crimes committed by government forces justify referral to the international criminal court. It argues that "the international community cannot afford to remain silent in the face of such deliberate attacks by the government of Sudan against its own people".

Deploring the "gross contempt" and "violent and unlawful acts" of government forces towards Unmis – including execution of a staff member, assaults, arbitrary arrests and detentions, and ill treatment "amounting to torture" – the report says: "Condemnation is insufficient… The international community must hold the government of Sudan accountable for its conduct and insist that it arrest and bring to justice those responsible."

National staff of international aid organisations have also come under attack. Unmis cites the case of a young Nuba woman arrested and accused of supporting the SPLM. Unmis human rights officers saw bruises and scars on her body consistent with her claim to have been beaten with fists, sticks, rubber hoses and electric wires.

Underscoring the need for the "independent and comprehensive investigation" Unmis recommends, the Observer has been told – by a hitherto impeccable source not connected to the SPLM/A – that 410 captured SPLM sympathisers were ordered executed on 10 June by Major-General Ahmad Khamis, one of four senior army officers sent to South Kordofan from Khartoum at the start of the war. The source told the Observer that the order to kill divided the military and security services. "Many disagreed with Khamis," he said. "The prisoners who were taken by military intelligence and the (paramilitary) Popular Defence Forces were murdered. Those with the National Intelligence and Security Service are still alive. There is a possibility some will see sunlight again…"

Khamis was one of the main implementers of a government jihad in the early 1990s that brought the Nuba people to the brink of destruction. On my first visit to SPLA-controlled areas in 1995, Khamis, then head of military intelligence, was repeatedly named as being responsible for torture and executions – including by his own hand.

With the Nuba region now closed to independent observers, and Unmis unable to move freely, it is impossible to verify or disprove claims like this. Significantly, perhaps, Unmis's human rights report makes mention of "fresh mass graves" seen on 10 June, the day of the reported executions, near Kadugli's police training centre. Unmis interviewed eyewitnesses who testified to two other mass graves: one in Tilo, four miles east of Kadugli, where an independent UN contractor saw government troops bulldozing bodies into the ground, and a second between army headquarters and Kadugli's main market. UN military observers attempting to reach the market site were arrested, stripped and threatened with execution.

Despite fighting talk by President Bashir on the eve of partition, senior government officials say a framework political agreement mediated by the African Union last month is still alive. Ethiopia and Rwanda have offered to contribute to a post-Unmis mission to monitor a cessation of hostilities, facilitate negotiation, and support the integration of the SPLA into the Sudanese army. The main point of contention is the timeframe for achieving this: the army wants weeks, the SPLA years.