The issue followed a testing glitch yesterday which meant some students were able to access their results a day early - only to have access revoked five minutes later.
Frustrated students took to Twitter today to complain about the website issues, with one saying they had "literally been trying for hours'' to log on.
Another said: "A bit slow would be an understatement.''
There was both elation and disappointment for those who did manage to log on.
Many students wanted to know how to get their exam results reconsidered, with one saying she was "one away from a excellence''.
NZQA said students have until February 18 to apply for reviews and reconsideration, or for standards to be re-checked or re-marked.
New Zealand is the only country in the world to return marked exam papers to students, which would take place later this month.
After the papers have been returned, scholarship students would be able to view their results online from mid-February.
Students can also request paper copies of their result summaries and achievement records from today.
An NZQA spokeswoman said national student achievement statistics would not be published until March.
Statistics released last year show achievement rates were generally on the rise in the five years to 2011.
The achievement rate at NCEA Level 1 increased from 73 per cent in 2007 to 77 per cent in 2011. The Level 2 achievement rate increased from 77 per cent to 82 per cent, and the Level 3 rate increased from 72 per cent to 75 per cent.
The achievement rate for University Entrance, which has different criteria to Level 3, remained roughly the same, at 67 per cent in 2011 compared with 68 per cent in 2007.
Girls did better overall, with 80 per cent achieving NCEA Level 3 in 2011 compared with 71 per cent of boys.
New Zealand European students had the highest achievement rate, at 81 per cent, followed by Asian students at 78 per cent, Maori students at 65 per cent and Pasifika students at 55 per cent.
Higher decile schools performed better than lower decile schools.