Human Rights Watch (HRW) on Tuesday criticised the arrests saying it feared both men - one of whom is charged with spying - were at risk of inhuman treatment, miscarriage of justice and possible execution.
"For the past year, the Sudanese government and its militias have waged war on the people of Darfur ... Now the government is persecuting those who are trying to protect these voiceless victims," said Sudanese researcher Jemera Rone, in a HRW statement.
Sudanese government officials were not immediately available for comment on the report.
HRW says a "government-led campaign" in Darfur has led to about 3000 civilian deaths.
Two rebel groups launched a revolt in arid Darfur a year ago, accusing Khartoum of neglecting the area and arming Arab militias known as Janjaweed to loot and burn African villages.
"Now the government is persecuting those who are trying to protect these voiceless victims"
The New York-based group said Salih Mahmud worked in Southern Darfur state providing legal assistance to people accused or convicted of crimes without a fair trial.
The statement said Mahmud was arrested on 1 February and had not yet been charged.
The rights group said the second detainee, Mudawi Ibrahim Adam, director of a voluntary aid group, was arrested on 28 December after returning to Khartoum from Darfur, where he had distributed aid to people made homeless by the fighting.
Adam faces charges including spying, waging war against the state and provoking hatred among religious sects. Some of the charges carry the death penalty, said Human Rights Watch.
United Nations officials have warned of a humanitarian crisis in Darfur with up to one million people displaced, and more than 100,000 refugees in neighbouring Chad. But the government says the fighting is under control and refugees are returning of their own accord.