The chairperson of the alliance, Deng Athuai Mawiir Rehan, said in October that his organisations treatment was "unbearable" and has called on the government to launch an "immediate investigation into harassment and targeted kidnapping of human and civil rights defenders".
"The intention is very clear. They just want to muzzle the alliance which will not work. Our government must investigate and take actions", Athuai told reporters on Sunday.
Ring Bulabuk, a defense lawyer who works with the alliance was kidnapped on 22 October in Juba by unknown armed personnel in civilian clothes. Relatives and friends say the men were members of South Sudan's security services.
Bulabek was later found abandoned at Juba graveyard in "a terrible shape", Athuai said, after being kept in an "undisclosed location" with no access to legal assistance and medical care until when he was found on Friday 26 October.
"There are people who do not understand what roles we play in the society. They see members of the alliance as threat. They do not see civil society as mirror through which people sees themselves", he said.
Despite, serious human rights issues, Athuai said that he believed South Sudan's leaders were striving to promote the supremacy of rule law, good governance, as well as improving transparency and accountability.
The the two abductions and beatings highlight the challenges facing South Sudan, which became the world's youngest nation when it seceded from neigbouring Sudan in July 2011 after two decades of civil war.