Northern Arab forces have been attacking the African Nubian tribe who live in along the new boarder of north and South Sudan.
From the BBC, we read more about the continued fighting in Sudan.
A UN spokeswoman said the train was attacked by Misseriya gunmen in South Kordofan state on Sunday, although this was denied by a Misseriya leader.
At least 70,000 people have fled recent fighting in South Kordofan, which borders South Sudan.
Tension has been rising ahead of the south's independence next month.
Another 100,000 people have been forced from their homes after fighting in the disputed town of Abyei, near South Kordofan.
"A train transport of southern Sudanese returnees going from Kosti to Wau was attacked by Misseriya militia," said UN spokeswoman Hua Jiang.
However, Misseriya leader Mohamed Omer al-Ansary said the attack had been carried out by rebels in the neighbouring region of Darfur, where a separate conflict broke out in 2003.