Students from Southern Sudan claim they are being targeted by Khartoom's security agencies and militia group trying to recruit them for attacks against their homeland.
But the allegations have been dismissed as baseless by the Sudanese government.
Besides being the economic nerve center, the Sudanese capital was also home to thousands of students from Southern Sudan seeking tertiary education before the split last year.
After the referendum that saw 99 percent voting for secession, there was a mass exodus of southerners trooping back to their homeland.
Khartoum by the virtue of it being the capital had more furnished educational infrastructure than Juba, the capital of the new, South Sudan.
However, many students remained in Khartoum to finish their studies after independence.
Now the students say they are being forcefully recruited into militia groups so that they fight against their own government.
A 19-year old student, Henry Obong studying in Khatoum said he was arrested and held in a safe house for several days before being informed that he had been recruited and was to undergo military training.
"I was shocked when I was told that. I pretended as if I was interested and managed to escape from them when they relaxed," Obong revealed.
Another student, George Price studying at the University of Bahari in Khartoum told a similar tale.
Speaking at a press conference organised by the Sudan People's Liberation Movement, (SPLM) in Juba last Saturday, Price claimed South Sudanese students living in Khartoum were arrested by Sudanese authorities.
"The Sudan government in Khartoum uses militia groups to forcefully recruit South Sudanese nationals," he said.
"They later take them to southern Kordofan and southern Blue Nile for military training and then sent to fight a senseless war against Southern Sudan."
Price narrated how he was arrested last month alongside seven other Southern Sudanese students but managed to escape with three colleagues.
"Things are not easy for southern Sudanese students studying in Khartoum," he said.
SPLM secretary for information Bol Makueng condemned the alleged harassment.
"What they are doing is not good at all. They are attempting to make South Sudan a failed state," he said.
He called upon the international community and human rights organisations to investigate the allegations.
But a Khartoum government security official, Ali Kassim denied the allegations.
"It is not true that Southern Sudan students are being mistreated in Khartoum.
"That is propaganda meant to make us look bad before the international community," Kassim said.
An estimated 600,000 people from South Sudanese still live Khartoum, according to Makueng.
