IOM Information Officer for South Sudan Matthew Graydon said there are nearly a quarter of a million South Sudanese in the north, including 40,000 who are living in deplorable conditions in Khartoum.
Another 20,000 are in a camp just inside South Sudan, in Upper Nile state, Graydon said.
The IOM is "working actively with the government to try to assist these people and move them on" to their final destinations in South Sudan, Graydon said.
IOM officials joined representatives of the British government and from UN agencies on a visit to two areas in Khartoum, where an estimated 40,000 South Sudanese are living in makeshift shelters, waiting to return to South Sudan.
"The mission found thousands of residents living in precarious conditions with limited food, water, healthcare and sanitation," the IOM says on its website.
"Shanties made of plastic sheeting, wood and scavenged materials provide them with little protection from the elements, particularly during the rainy season. With no sanitation facilities, defecation in the open is common, which poses huge health risks especially when flooding occurs," it says.
Thousands of South Sudanese moved out to the open areas in Khartoum in late 2010 "to take advantage of planned return movements" that were supposed to be organized by the two governments, the IOM says.
Juba and Khartoum never reached an agreement on the returns and most of the waiting South Sudanese never made it home.
Other South Sudanese moved out to the open areas in Khartoum because they lost their jobs following South Sudan’s independence, and could no longer afford to pay rent.
More than 700,000 South Sudanese returned from Sudan to South Sudan before a 2010 referendum on independence for the south, 42,000 of them with help from the IOM.
Many of the estimated 230,000 South Sudanese who are still in Sudan want to return to the south, which became independent in July 2011, but don't have the means to do so.