Many refugeees left behind an easier life in Khartoum, the capital in the north, to return for the census, which will be carried out nationwide from April 15 to 30, Puoc said.
Sudan's census, the first since 1993, is to provide the most complete count to date of Sudan's estimated 39 million people and redraw or confirm the power-sharing balance between northerners and southerners.
Puoc said about 1.5 million southerners remain in Khartoum and an unknown number elsewhere in the north who are not registered.
The UN refugee agency has also said it is expecting a surge in repatriation movements from countries bordering southern Sudan ahead of the census.
The UNHCR last week reported 15,700 organised returns since January, amounting to three times the number during the same period last year.
The refugee weekly return rate increased from 600 people at the beginning of the year to 3,000 at the beginning of March, Fatoumata Kaba, the agency's spokeswoman, said.
Of the returnees, close to 10,000 were from Uganda and February returns from Kenya surged to 2,500, surpassing the 600 monthly average.
"The trend is expected to continue over the coming months," Kaba said.