The United Nations has sent a second observer mission into the Darfuri town that was burned down and looted while under Sudanese government control.
Rebel forces blame the government and Janjaweed militias for the destruction of Haskanita - and for last week's attack on an African Union base.
A statement from the Sudanese armed forces said attempts to implicate them are "unfortunate and illogical".
The UN observer mission did not say which forces destroyed Haskanita.
The government statement - from the office of the armed forces' spokesman - said the army had "fully carried out its role of pursuing those accused of the recent massacre", i.e. the attack on the AU base on 29 September which killed 10 peacekeepers.
"The burning of Haskanita is an issue relating to the area's internal security," the statement added.
One Darfuri rebel group, the Justice and Equality Movement told the BBC that there was proof that the government forces were involved, thanks to a photograph of a green military tank in the town.
The London spokesman for the JEM, Haroun Abdul Hameed, said "only Sudanese army tanks are green", "the rebels have no tanks" and the "African Union vehicles are white".
He admitted that this was the only evidence the rebels have to suggest that government forces, or their militia allies, were responsible for the razing of Haskanita.
Claim and counter-claim
The UN said that only the school and mosque were left standing in the town, which had been home to 7,000 people though many fled when the AU base came under attack on 29 September.
The destroyed town was close to the base where 10 AU soldiers died
The commander of the AU-UN peacekeeping force blamed the attack on a rebel splinter group "who broke away from a faction called SLA United".
Another leading rebel, Suleiman Jamous, who represents the Southern Liberation Movement and is based in Chad, said he too believes the Sudanese army carried out the attack on Haskanita and said up to 100 people were killed.
The UN has dismissed this claim.
For its part, the JEM denies its forces had anything to do with the attack on the AU base and alleges that too could also have been the work of government forces.
"Only government fighters were in the area," Haroun Abdul Hameed said, "the rebels had withdrawn".
By next year the UN and AU are meant to have deployed the world's largest peacekeeping force - 26,000 troops - to Darfur.
The hybrid force will absorb the 7,000 AU troops in the region who have struggled to protect civilians, admitting they are outmanned and outgunned.
At least 200,000 people have died in Darfur during a four-year conflict and more than two million have been forced from their homes.