The ministry's decision will impact over 600 students in Wau's Standard Secondary School, located in the capital of Western Bahr-el-Ghazal State; Juba High School in Bor, situated in the capital of Jonglei State in eastern South Sudan; and Ganyliel Secondary School in Unity State, in the northern region of the country.
Additionally, the examination board canceled the results of 46 students found in possession of smartphones and other materials used for cheating during exams.
Twenty-year-old Ajok Nyok Deng, who took the secondary school exams at Juba High School last year after giving birth, is among the students impacted.
Deng said the process of taking the exams was to allow her to prepare for her future.
"Now, I don't know what I will do, and for now, I don't have any money to go back and sit again," she told VOA.
Students who were affected by the ministry's decision are now required to retake the exams to qualify for university studies.
Standard Secondary School was cited due to severe violations of examination rules and regulations, involving acts such as stoning security personnel and examination monitors.
During testing last year, students resisted being overseen by exam invigilators and ended up throwing stones at the monitors.
Juba High Secondary School and Ganyiel Secondary School were also found to have grossly violated examination rules and regulations by chasing examination monitors, leading to injuries of security personnel.
Martin Tako, South Sudan's deputy minister for general education, stated that the decision was made to prevent future abuses by students and teachers during examinations.
Tako emphasized the measures taken to safeguard the exams, stating, "This time we have tightened the examination, nobody can steal the examination from the examination council, and we print them in London."
Akuei Philip Nyok, headmaster of Juba High School, expressed that he had foreseen the cancellation of the results.
"The decision was made based on what the students had done because fighting with national monitors and the rest of security plus invigilators, that one is not allowed by law," he explained.
"There is nothing we can do rather than calling the students to sit again."
South Sudan's top-performing schools in the 2022 Certificate of Secondary Education examinations were from Eastern Equatoria State, followed by Central Equatoria State.