South Kordofan has been ravaged by a war between the government and JEM rebels since 2003, which according to the UN has left 300,000 people dead and 2.7 million homeless.
The Sudanese deployment raised tension in the province, as there have been unconfirmed rumours circulating among UN agencies and government bodies that a JEM force crossed into the region around three weeks ago.
No one was available to comment from the rebel movement, however, their spokesman last week refused to "confirm or deny" a new JEM push into South Kordofan.
The north and the south have had a troubled relationship since the signing of the 2005 peace deal. Their troops have clashed, most recently in May over the oil town of Abyei, which both sides claim.
Under the deal, the north's Sudan Armed Forces were to be reduced to pre-war levels in South Kordofan, one of three "transitional areas" bordering the south.
The International Crisis Group think tank said in October the 2005 peace deal was at risk in South Kordofan, which had "many of the same ingredients" that produced the raging conflict in the neighbouring region of Darfur.