The United Nations and African Union have condemned the Sudanese army and Janjaweed militias for attacking rebels in Darfur's Jebel Moon area.
One faction of the SLA is co-operating with the government
They denounced the government violation of a May peace agreement and expressed concern for the safety of civilians.
This is the first time since the peace deal that the Sudanese army has been confirmed as fighting in Darfur.
The attack was against the rebel Justice and Equality Movement, (JEM) which did not sign the deal.
Some 2m people have fled their homes in Darfur since conflict began in 2003, and tens of thousands of people are reported to have been killed in ongoing violence.
Both government and militia troops had been observed massing near the western town of Geneina before the attack on Friday.
An assortment of armed groups that remained outside of the peace agreement, including Chadian elements, are known to be taking shelter in the Jebel Moon mountains.
The attack is confirmation that Darfur's conflict has changed in nature, the BBC's Jonah Fisher reports from Sudan.
The two signatories to the peace agreement - the government and the Minni Minnawi faction of the Sudan Liberation Movement - are using the agreement as a springboard to attack those outside the deal.
The SLM Minnawi has launched a wide-ranging offensive against their former rebel allies and supporters, leaving at least 80 people killed and thousands displaced.
JEM spokesman Ahmed Hussein Adam said the Sudanese government was systematically attacking groups who had refused to sign for peace.
SLM Minnawi was the main rebel group in the Darfur conflict, and the only one that signed the deal on 5 May with the Sudanese government.