By Denis Dumo
JUBA (Reuters) - South Sudan's president signed a peace deal on Wednesday to end a 20-month conflict with rebels, but he told regional African leaders at the ceremony that he had "serious reservations".
President Salva Kiir, who has led South Sudan since it seceded from Sudan in 2011, had asked for more time for consultations last week, drawing threats of U.N. sanctions if he failed to ink it within a two-week deadline.
"With all those reservations that we have, we will sign this document," he told African leaders who had gathered in Juba for the ceremony, speaking shortly before he signed.
His long-time rival and rebel leader Riek Machar, who is expected to become the First Vice President under the deal, put his pen to the document last week in the Ethiopian capital.
The conflict erupted in December 2013 after a power struggle between Machar, an ethnic Nuer, and Kiir, from the dominant Dinka group. Fighting has increasingly followed ethnic lines.
Thousands of people have been killed, many of the 11 million population have been driven to the brink of starvation and 2 million people have fled their homes, often to neighboring states. It has unsettled an already volatile region.
The deal follows months of on-off negotiations, hosted by Ethiopia, and several broken ceasefire agreements.
Rebels said they captured a town south of Juba on Wednesday after their troops were attacked, and that there had been other bout of fighting with government forces.
Kiir told the ceremony that rebels launched a raid in the north of the country earlier in the day. "Now you can see who is for peace and who is for continued war," the president said.
Machar was Kiir's deputy until he was sacked in 2013. Under the deal, he is expected to become Kiir's top deputy again.
Kiir gave a document to regional leaders listing his concerns. Mediators have said Kiir had voiced concerns about a demand that Juba become a demilitarized zone and conditions that he consult the first vice president on policy.
Machar has also conveyed doubts about aspects of power sharing.
At the ceremony, Kiir said he had faced intimidation during the peace process and added negotiations were "carelessly" handled by regional and world leaders, saying a poor agreement could backfire on the region.
Kenyan President Uhuru Kenyatta said it was a "happy day for us in the region" that the deal had been signed, and that the South Sudanese leaders now needed to focus on the future.
His comments were echoed by Ugandan President Yoweri Museveni and Ethiopian Prime Minister Hailemariam Desalegn.
The United States had proposed a U.N. arms embargo and more targeted sanctions from Sept. 6 unless the pact was signed by the 15-day deadline given to Kiir last week.
(Additional reporting by Aaron Maasho in Addis Ababa and Drazen Jorgic in Nairobi; Writing by Edmund Blair; Editing by Mark Heinrich)