Just a week after saying that the only outcome he would accept from the landmark referendum due in January was a vote for unity, Beshir insisted his government was working for peace.
"There will be no return to war," the official Suna news agency quoted Beshir as saying. "The government is working to keep the peace.”
The January referendum on independence for the south is the centrepiece of a 2005 peace deal which brought an end to Africa's longest-running civil war in which an estimated two million people died.
"Despite our commitment to the Comprehensive Peace Agreement, we will not accept an alternative to unity," Bashir had told MPs in Khartoum on 12 October.
On Tuesday, Defence Minister Abdel Rahim Mohammed Hussein hinted that the referendum could be delayed in the face of persistent wrangling between northern and southern leaders about the demarcation line between the two regions.
Southern leaders have warned that if there is any major delay by the Khartoum government in organising the referendum, they will go ahead and hold a vote of their own.