Malcolm McDonald, president of SAGT, said: "In the science baccalaureate, geology and management of environmental resources, mostly taught by geographers, and fabrication and welding engineering - which had just 13 students last year - are included, but geography is not."
Schools Minister Maureen Watt has defended the Government's subject criteria for the science and language baccalaureates, but said she had not ruled out plans to develop similar qualifications in other subjects areas.
SAGT, meanwhile, has welcomed amendments by the Scottish Qualifications Authority to the Higher and Advanced Higher geography exams to reflect the Government's sustainability agenda and growing awareness of "green" issues.
An SQA spokesman said: "The 2008-09 courses for Higher and Advanced Higher Geography are intended to reflect our aim to make all qualifications as relevant as they possibly can be in the wider world. The broadening of the study of global climate change to include its consequences as well as its causes, together with the opening up of the topics which candidates can choose to study at both levels - which may be studied for essay purposes - is part of that strategy."