They had fabricated exam results, as well as other issues, said Higher Education Minister Blade Nzimande.
The institutions have failed to submit audited financial statements since 2020, the education department said.
The colleges are owned by Educor, one of the largest private education providers in southern Africa.
Educor is yet to respond to a BBC inquiry about the allegations.
It runs educational institutions on more than 60 campuses in South Africa and internationally.
The colleges, Damelin, CityVarsity, Icesa City Campus and Lyceum College located around the country, have been given until the end of the year to cease operations.
Higher Education Minister Blade Nzimande told journalists that after a large-scale investigation into the colleges, serious issues had been brought to his attention.
Mr Nzimande labelled the colleges “dysfunctional” due to a number of complaints received from students and workers, “most of which remain unresolved”.
Some students complained about the poor quality of teaching and learning, lack of administrative support and lack of professionalism, the minister said.
There have been allegations of non-payment of staff salaries and corruption, he added.
The Educor institutions also inflated their numbers so as to hide their declining student population, according to the minister.
The provider said it had 50,000 students, however its 2022 annual reports indicate a total enrolment of 13,096 students across all four institutions, he said.
Mr Nzimande also said that some students’ examination marks were fabricated.
“That’s the worst sin that can be committed by an education institution, whether public or private — you cannot just lie and give students marks based on scripts that were never marked,” the minister said.
Additionally, the colleges are said to have failed to submit audited annual financial statements and to obtain tax clearance to prove their financial viability.
The Department of Higher Education and Training has been in the process of deregistering the private institutions since July 2023 but the final decision was made last Friday.
More than 13,000 students will be affected by the decision, with some left stranded without accommodation.
Education authorities have urged affected students to transfer to other institutions.
Parents have been visiting the colleges to demand answers and fees that they had paid for the year’s tuition.
The South African Union of Students welcomed the deregistration of the colleges, saying the decision was in the best interests of students, local media reported.
The South African Federation of Trade Unions (Saftu) said Educor had been “mistreating employees and students for too long”.