It said that PT3 is carried out in the same way as any final examination in schools using standardised questions.
"Therefore, there is no need for candidates to resit the PT3," it said in a statement Friday (Oct 4).
The ministry's statement follows allegations that some PT3 papers, including English, Mathematics and Geography, were leaked on social media before students were due to sit for the exams.
The ministry also said that the examination will go on as scheduled and students will sit for the remaining Science, History, Religious Studies and Bahasa Melayu papers between Oct 7 and Oct 9.
It also explained that the PT3 was a central examination within the school-based assessment system.
The central exam is administered by schools based on a standardised scoring instrument guide prepared by the Malaysian Examinations Syndicate.
It added that the PT3 was an academic component in the school-based assessment system for lower-secondary students, and both the Examinations Syndicate and schools have shared accountability in implementing them.
The ministry also said candidates should be allowed to sit for the exams calmly and not raise any issues that could worry both them and their parents.
It was also reported that many people received a "media statement" allegedly issued by the ministry that the PT3 English paper would be repeated on Oct 10 due to a leak but the ministry quickly dismissed the rumour.
The PT3 replaced the Penilaian Menengah Rendah (PMR) exams in 2014 and is one of the four assessments under the overall school-based assessment system.
The other three components are the school assessment; assessment of physical, sports and co-curricular activities; and psychometric assessment.