The acknowledgement that mistakes were made followed a flood of complaints to the exam board from students and parents for whom the college exam is the culmination of 10 years of gruelling, high pressure study and substantial financial sacrifice.
"I express deep regret and recognise an urgent need to improve the question-making process," Education Minister Hwang Woo-Yea said in a televised statement.
"We will investigate the root cause of the problem," Hwang said.
Success means a secured place in one of South Korea's elite universities - a key to future careers as well as marriage prospects.
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With so many taking the exam - and so many scoring highly - one small error can put a student on the wrong side of the extremely thin cut-off line for a top university.
Hence the uproar over the two suspect multiple-choice questions - one in the biology exam and one in the English language paper.
South Korean media reports estimated that as many as 4,000 students would receive a higher overall grade as a result of the decision.
Kim Sung-Hoon, head of the Korea Institute for Curriculum and Evaluation (KICE) which administers the exam, said he would resign.
"We did our best this year to prevent erroneous questions ... But again there were faulty questions, causing chaos and inconvenience among exam takers, their parents and teachers," Kim said.
A similar row over a question in the geography paper in the 2013 exam took a lot longer to resolve.