Salva Kiir accused the Khartoum government of never making "unity an attractive option" for the mostly Christian and animist southerners.
Sudan's savage two-decade civil war ended in a 2005 peace agreement that included a provision for a 2011 referendum for the southerners to choose if they wanted to remain in the country.
A southern decision to secede could well reignite one of Africa's worst conflicts, claiming 2 million lives.
"There is hope that Sudan may stay united if the other party is serious," Kiir told reporters after a meeting Monday with Egyptian President Hosni Mubarak to discuss Sudan's conflicts.
Kiir also accused the northern government of failing to implement fully the peace agreement including the demarcation of the oil-rich border region between the north and the south.
He said the maps should be ready next month.
The peace deal put an end to the 21-year-old civil war between the mostly Arab and Muslim north and rebels in the Christian-animist south that left 2 million people dead and 4 million displaced. But the deal is plagued by distrust between the two sides and has repeatedly threatened to unravel, bringing to the two sides to the brink of war.
Under the deal, Sudan is to hold key parliamentary and presidential elections in April — the first national elections to include all of South Sudan in four decades — as well as the referendum.
In both cases, smooth elections are seen as crucial for keeping peace. But disputes have arisen between north and south over census results, which are the basis for drawing election constituencies. The two have also yet to agree on north-south borders, an already explosive issue because it also involve dividing oil and grazing rights.
The U.S. has been actively pushing the two sides to iron out their differences over the votes, considered vital to prevent a return to war.
A disagreement over how to conduct the referendum has been settled recently. But southern lawmakers are now boycotting parliament to pressure the northern government to discuss election-related laws, such as press freedom and a security bill, ahead of the vote.
In Monday's statement Kiir refused to postpone both the election and the referendum.
"So far we have agreed to hold the elections in 2010. I hope this happens."