Lawyers believe that they are so vague as to make "objective and fair assessment (of applicants) difficult", making it "more likely that discrimination will occur".
It will be harder for part-time and job-share teachers to show their contribution to pupils' progress. Teachers who have taken a job break - particularly women returning from maternity leave - face similar problems, making claims for indirect sex discrimination possible.
The legal loopholes, exposed in advice obtained by the National Association of Schoolmasters Union of Women Teachers, may leave schools and local authorities facing a deluge of discrimination claims.
Nigel de Gruchy, general secretary of the NASUWT, said: "The Government seems content to issue a flawed scheme to governing bodies and LEAs, leaving them to face the possible legal consequences and claims for substantial damages."
The warning came after heads raised fears that their role in assessing teachers for the new pay threshold would be impossible in the very schools where the Government wanted most to raise standards - Fresh Stat schools.
The Secondary Heads Association's annual conference last weekend heard concerns that heads of new or Fresh Start schools had no results or other evidence on which to judge applications.
Teachers might have to wait a year to apply.
Judith Mullen, head of New College, Leicester, which was created from the amalgamation of three schools, said newly-appointed heads would not know enough about their staff.
A spokesman for the Department for Education and Employment said: "The head's task is to assess application forms and comment on whether the evidence is sound, representative and at the level required to meet the standard.
"If some or all of that evidence relates to previous schools then the head should contact previous schools if necessary."
Two further concessions on the new system, due to be introduced in September, have been won. Heads receiving more than 40 threshold applications will have an extra half-term to assess their staff.
The Government will also give schools an extra pound;20 million to free up time for the process.
SHA also wants a mandatory pound;2,000 pay rise for deputy heads following a flow of angry calls to its hotline from deputies who fear they have been overlooked.