Southern officials sent to Sudan have been reassuring their people and telling them not to panic, a non-governmental worker said, as Sudan's interior minister, Ibrahim Mahmoud Hamid, confirmed the deadline.
The minister said police stations would be open for those wishing to register as northern residents, the official SUNA news agency reported.
But officers at two stations said they had only heard about the initiative on the news, and no Southerners were there to register.
The April 8 time limit ended a grace period after South Sudan separated last July in the wake of an overwhelming "yes" vote in an independence referendum that followed Africa's longest civil war.
The 22-year conflict killed two million people and drove many more to the north.
While hundreds of thousands have already returned to the South, an estimated 500,000 others remain in Sudan, waiting for clear direction on what to do.
Confusion remains especially among the many Southerners who have not been able to obtain South Sudanese passports, said Reverend Iskander Ali, an ethnic Southerner who preaches at All Saints Episcopal Cathedral in Khartoum.