All NCEA Scholarship exams have been postponed across the country, with other exams in quake-affected areas also interrupted.
A magnitude 7.5 earthquake struck near Hanmer Springs just after midnight and a number of aftershocks have rattled the country since.
Massey University has put off exams in Wellington and Manawatu, though exams in Auckland will go on.
Exams for distance students scheduled for Christchurch and Lower Hutt will also be postponed as will places which are also affected by earthquakes.
"We're aware this has caused significant disruption to many students' study with power outages and evacuations in some places," Assistant Vice-Chancellor Operations, International and University Registrar Stuart Morriss says.
NZQA initially said NCEA and Scholarship exams will continue for schools which haven't been affected by earthquakes. But in a later update, announced all Scholarship exams in all schools and exam centres were on hold for the day.
For those who have been affected, an "emergency derived grade" process is available for those who are disadvantaged.
NZQA deputy chief executive Kristine Kilkelly says the process involves schools using results of practice exams to determine a student's final grade.
She told Paul Henry students who felt their performance was affected by the "distress" of the incident could also apply for a derived grade.
Ms Kilkelly said postponing all exams would have been more disruptive to the thousands of students sitting tests.
"It was difficult in this timeframe to reschedule the exam without causing probably more disruption to other students as well. The exams go on in a tight schedule until early December," she says.
"It would also mean a potential slowdown in marking and results processing which in itself causes additional stress to students."
The Scholarship exams affected a limited number of students, and aren't covered by the emergency derived grade process. Those sitting the exams give monetary rewards to students.
Massey University's Wellington campus will be closed until at least midday, while the Manawatu and Auckland campuses will remain open.
Victoria University in Wellington will also be closed until midday while buildings are checked, however there appears to be no significant damage.
Agricultural and Horticultural science, as well as classical studies and music across all levels were supposed to be sitting today.
Some schools in the quake-affected areas which participate in the Cambridge International Exams will also be affected.
The Association of Cambridge Schools in New Zealand says if students can't get into their schools there is also a system for "special consideration", similar to the derived grade process, available to students.
Schools from North Canterbury to Wellington have been advised to stay closed until buildings can be checked.
The Ministry of Education has released advice for schools and early childhood centres (ECE):
NZQA has closed its office for the day, as they await routine building safety inspections.