Addressing a news conference in Nairobi, the UN High Commissioner for Refugees (UNHCR) Antonio Guterres also appealed to regional governments to stop treating refugees as terrorists but instead open their borders to more people fleeing the conflict.
"I want to appeal to international community to strongly invest in South Sudan and to do it quickly ... in education, infrastructure, in health and in job opportunities to enable the people going back to have better perspectives for their future lives," Guterres told journalists in Nairobi.
"There is a huge challenge for construction in South Sudan and not reconstruction because there has virtually nothing in terms of infrastructure to improve living conditions of the returnees," he said.
"The refugees returning to South Sudan really need international support on a very sustained basis, otherwise there is a risk they could be uprooted again."
The UNHCR chief said repatriation efforts from neighboring countries have been stepped up before a census planned for Southern Sudan in early next year.
Guterres termed the ongoing repatriation exercise to Southern Sudan from neighboring countries a positive step, saying it was helping play a critical role in rebuilding the vast region.
The UNHCR chief said it was clear that the international community did not know how to handle the transition from war to peace and from emergency relief to development.
"The international financial and development institutions work too slowly for places like South Sudan. We need new forms of intervention, including the help of foundations, because the existing system is often simply too slow to benefit the people who need help," he said.
"This year, we are gearing up our capacity to bring more and more people into Southern Sudan and this is evidenced by the figures in the first four months of this year. We have brought more people than all of last year. This shows acceleration is taking place," he said.
Guterres said UNHCR would continue to provide transport for those willing to go back to Sudan throughout the rainy season to ensure as many people as possible were repatriated.
"As a matter of fact, our return is voluntary, is well informed and is in sanity and dignity. We need to respect the free will of the people. This year, UNHCR has already organized the repatriation of 35,000 people to Sudan, up from 20,996 last year," he said.
Guterres said the signing of the peace agreement in 2005 and the planned census in 2008 have encouraged more refugees to go back to South Sudan to participate in the reconstruction of their country.
"It is naturally that many people want to participate in the reconstruction and the institutions of their country. The repatriation so far is positive because its voluntary and the number of returnees are picking up," said Guterres.
The signing of the Comprehensive Peace Agreement for South Sudan in January 2005 ended a 21-year civil war between the north and the south and paved the way for the repatriation of refugees in camps in neighboring countries.
The first UNHCR-organized repatriation convoy took place in December 2005 from Kakuma camp in Kenya to Bor and Kapoeta areas in south Sudan.
Since then, Guterres said more than 155,000 Sudanese refugees from at least seven countries in the region have come back to their homes in Southern Sudan and Blue Nile State, including 64, 000 through UNHCR's voluntary and assisted repatriation operation.
Over 300,000 refugees still remain in camps in neighboring countries. UNHCR plans to bring home a total of 102,000 refugees from countries of asylum in 2007.