EAL (English as an additional language) and bilingual support teachers are concerned that the programme, which requires them to assess bilingual pupils as being in one of five categories, will damage race equality.
The Glasgow local association of the Educational Institute of Scotland is calling on the union's national officers to intervene with the Scottish Executive and to clarify with the Commission for Racial Equality whether the initiative contravenes race relations laws.
Around 9 per cent of Glasgow's school population is bilingual - a mixture of Scots-born ethnic minorities, families attached to universities and others who have come to the city as asylum-seekers.
The city has the only Gaelic-medium primary school in Scotland and plans to open a 3-18 Gaelic-medium school. Gaelic-medium pupils are also covered by the Executive's policy.
The Executive said the ScotXed programme (Scottish Exchange of Educational Data) was simply part of the latest school census. "It will be used to give us an indication of the number of pupils who have English as an additional language and might therefore have additional special needs."
However, Larry Flanagan, a member of the EIS national executive council and a teacher at Hillhead High in Glasgow, said that teachers believed the programme was crude and "fundamentally flawed" because it did not differentiate between two distinct categories of bilingual learners - new arrivals and British-born bilingual learners.