Their landmark action follows claims that the Executive-backed survey of teachers is "a fix".
Michael Doig, head of Cumbernauld High and a prominent member of the Headteachers' Association of Scotland, described the Executive's poll carried out by System Three as "not capable of reflecting the answers teachers wanted to give".
The Educational Institute of Scotland and the Scottish Secondary Teachers' Association have now commissioned Mori, a rival polling organisation. It will combine telephone questions with back-up focus groups of practising teachers and lecturers. The findings will be available at the en of January.
Ronnie Smith, EIS general secretary, said: "The EIS and SSTA are working together to ensure that teachers and lecturers with direct experience of Higher Still are fully included in the consultation process before changes are proposed to Higher Still for the 200102 session. The survey will provide a clear statement of how the teaching profession wants Higher Still to be taken forward. It will be impossible to ignore."
David Eaglesham, SSTA general secretary, said: "This joint survey will produce an incontestable picture of the position of secondary teachers and will enable the two unions to shape the future of this vital process for the benefit of our young people."
The Executive is surveying 200 schools on Higher Still issues and 57 on internal assessment.