Changes to exams for 16 and 18-year-olds at the same time as an overhaul of the curriculum for 11 to 14-year-olds will place an unacceptable burden on schools, it warned.
Steve Sinnott, NUT general secretary, has written to Ruth Kelly, the Education Secretary, urging her to provide extra funding or risk a repeat of the disruption which, three years ago, left hundreds of teenagers with the wrong A-level grades and contributed to the resignation of Estelle Morris.
His letter follows concerns expressed by the Qualifications and Curriculum Authority that the changes will place "unprecedented pressures on schools".
Mr Sinnott accused the Government of having "no coherent and resourced plan" for training teachers to implement the reforms.
Changes scheduled for 2008 include the introduction of specialised diplomas for 16 to 18-year-olds, a revised key stage 3 national curriculum and new "functional" tests which will be incorporated into English, maths and information and communications technology GCSEs.
Mr Sinnott said: "The intensity of the reform process, without an underpinning of financial provision - particularly for professional development and for securing time for preparation during the school day - combined with the bunching of reforms facing secondary schools and colleges leading up to the academic year 2008-09, is unacceptable.
"I do not think that any of us, and certainly not parents and young people, can afford to find themselves in a situation similar to the turbulence and disruption caused by the Curriculum 2000 reforms."
He called on Ms Kelly to conduct an audit of the financial and training implications of the reforms and to set up a 14 to 19 implementation body to oversee them. New qualifications should have a minimum lead-in period of 10 years, he said.
The NUT's concerns follow the December publication of the Government's 14 to 19 implementation plan. Ministers have promised five new vocational diploma courses to improve work-related education for 14 to 19-year-olds by 2008. By 2013, every teenager will be offered the chance to take a work-related diploma in one of 14 subjects, as an alternative to GCSEs and A-levels.
Schools, colleges and employers will be expected to work together to teach the new exams, and the Government has pledged to train 5,000 new staff to teach them.
A-levels will be redesigned to include new, tougher questions that help universities select between high-achievers, and introduce an extended project.