A poll of thousands of secondary teachers found nearly 80% said they were not confident in assessing pupils for the new National 4 and National 5 exams - which replace Standard Grades.
The survey by the Scottish Secondary Teachers' Association (SSTA) also found 60% were not confident in delivering course materials for the qualifications.
The poll - which was based on returns from around half of the 5500 teachers questioned - is another blow to the National exams, which were introduced as part of the new Curriculum for Excellence (CfE) reforms and will be sat by some 54,000 15 and 16-year-old pupils from April.
The survey also throws doubt on the roll-out of new Higher exams which will be sat next year.
Alan McKenzie, the SSTA's acting general secretary, said: "Such alarming rates of lack of confidence must be acted upon because if a teacher lacks confidence then this will be quickly transferred to young people.
"Throughout the implementation of CfE the SSTA has attempted to signal real concerns about progress and it is clear that the great area of dissatisfaction is with Education Scotland and the SQA. We have been careful about appearing alarmist and at all times wished to contribute positively to the successful outcome of this curricular initiative. There is still time to achieve this."
Dr Janet Brown, SQA chief executive, said the SQA's priority was to work in partnership with teachers to listen to their concerns and provide the additional support needed.
She said there was "clear evidence" in many schools and colleges of a good understanding of the expected standards.
A spokeswoman for Education Scotland stressed that the organisation had provided a range of support to help teachers prepare.
Meanwhile, the Educational Institute of Scotland has warned that a "toxic combination" of curriculum change and budget cuts is putting teachers under increasing pressure. The EIS claimed some of its members were now at "breaking point".