At least 2,900 persons had crossed into the neighbouring Uganda since Friday in which more than 90 per cent were women and children, Xinhua news agency reported.
"The number of people seeking shelter and safety in Uganda from South Sudan has risen significantly in the past few days and we believe the influx will keep growing in the days ahead as tensions remain high across the border," UNHCR said in a statement.
As the restrictions have been eased and the 200 km Juba-Nimule road has been cleared of the checkpoints, more persons were expected to flee to the East African country.
"As a result, more people are now coming by truck, and this explains the rising numbers of arrivals. Many are also bringing belongings," said UNHCR.
The security situation remains volatile and fighting could return at any time while refugees talk of an increase in looting.
Over 6,000 South Sudanese were staying in the Pagiarinya refugee settlement in Uganda. The recent evaluation reveals the settlement has capacity for another 6,500 persons, the UNHCR said.
"An inter-agency site assessment mission, including officials from the Government of Uganda Office of the Prime Minister and UNHCR, are currently visiting sites to identify areas suitable for establishing new settlement areas," said a statement by the UNHCR.
At least 300 persons were killed and over 10,000 fled their homes after a clash between government troops of President Salva Kiir and forces loyal Vice President Riek Machar in the capital.
"The fresh displacement will put a further strain on UNHCR's resources for the South Sudan operation and our ability to provide timely and life-saving assistance, especially with access to Juba difficult," it said.
On July 15, UNHCR presented a revised appeal for its South Sudanese refugee operations, seeking $701 million though the earlier appeal for $608 million was only 17 per cent funded.
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