"Jem troops, along with 40 artillery tanks from the Chadian forces, and about 80 Jem vehicles, attacked this position," al-Agbash said.
"Our forces fought fiercely and repelled three violent attacks.
"Initial reports confirm that 43 enemy soldiers from JEM were killed, and 54 wounded. Our troops reported 20 martyrs and 31 soldiers wounded."
"I would like at the outset to confirm that any reports about the so-called Justice and Equality Movement controlling the Umm Baru village are totally baseless."
'Fog of war'
The region's joint United Nations-African Union peacekeeping force (Unamid) had reported on Sunday that the rebels had overrun the army base.
But Kemal Saiki, the Unamid information director, said peacekeepers' reports had been confused.
"They did make a push for it, but they did not overrun the post. Put it down to the fog of war," he said.
Suleiman Sandal, JEM's head of strategic operations, told the AFP news agency that the garrison had been defeated, but his fighters had pulled out after government aircraft bombed the area.
"We destroyed completely the garrison of the Sudanese army in Umm Baru [then] the airplanes of the Sudanese army shot randomly," he said.
"We have some people who died, I cannot say the opposite."
Air attacks in Darfur are banned under UN security council resolutions and a series of failed ceasefires, but Khartoum has in the past reserved the right to attack Jem and other rebel groups that did not sign a peace deal in 2006.
Sandal said that his group was braced for more fighting after hearing that Sudanese army units had left el-Fasher, the capital of Darfur, and were headed to the area.
"Now we are preparing to face these mobile forces," he said.
Umm Baru, which is just 100km from the border with Chad, has seen a number of clashes between pro-government forces and Jem fighters over the past two weeks.
The latest round of peace talks between the Khartoum government and Jem leaders are due to begin in Doha, the capital of the Gulf state of Qatar, on Wednesday.
Ahmed Ben Abdallah Al Mohmoud, Qatar's foreign minister, was also planning to visit Chad in a bid "to solve the problems between the two countries", Sudanese state media said.
Tensions along the border between Chad and Sudan have been mounting for several weeks as each accuses the other of supporting rebel groups seeking to topple their respective governments.
Ndjamena has accused Khartoum of backing a recent offensive by Chadian rebels, while Sudan has said that Chad backs the Jem rebels.
Darfuri rebel groups took up arms against government soldiers and allied militias six years ago and up to 300,000 people are thought to have died in the ensuing violence, according to the UN.