The Educational Institute of Scotland (EIS), the country's largest teaching union, said a survey of members highlighted a raft of concerns over the introduction of National 4 and National 5 exams - which replace Standard Grades.
Survey responses show school staff struggling to understand the purpose of the changes and having little time to adapt their teaching techniques.
Many teachers also complained about unacceptable workloads as well as inadequate support from the Scottish Qualifications Authority (SQA), which has developed the new exams.
The concerns cover most subject areas with particular emphasis on English, maths, computing, physics, chemistry and biology.
This is the latest controversy to hit 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.
Larry Flanagan, general secretary of the EIS, said: "We are witnessing an unprecedented level of concern from our members in schools about the SQA. Over 80% of our local associations have contacted us directly about a range of issues including lack of clarity around procedures, inadequate support being offered, assessment overload, excessive verification demands, and poor exemplification of standards.
"Teacher anger and frustration is palpable. We are seeing schools criticising what is perceived as the failure of the SQA to deliver a coherent and workable CfE programme.
"The EIS has raised these issues with SQA and we appreciate that it is working hard to address concerns, but the simple fact is we are now halfway through the school session, literally weeks away from the first diet of exams, and there are still too many challenges in the system."
However, Dr Janet Brown, chief executive of the SQA, said the body would continue to provide support for schools over the coming months. She said: "The new Nationals are the latest step in the evolution of Scottish qualifications and we understand change always brings challenge.
"Our key priority in the coming months is to work with teachers to provide the additional support they need to ensure the Nationals are implemented to the benefit of all our young people."
A Scottish Government spokesman said teachers had been provided with unprecedented support for the roll-out of CfE.
He said: "This includes more than £5 million of additional funding since 2012, two extra in-service days, course materials for each of the 95 National 4 and 5 qualifications, and subject specific events for thousands of teachers.
"We will continue to listen to teachers to ensure they get further help if needed."
The SQA said almost 7500 teachers had attended 140 subject events for the new Nationals and SQA's Curriculum for Excellence liaison team continues to visit every school across Scotland to meet teachers and parents, explain the changes, answer questions and gather feedback to gauge what further support is needed to deliver the new qualifications.