The targets' initiative will merely "divert teachers' attention from teaching and learning and into bureaucratic procedures", the union says in its response to the Scottish Office consultation.
The EIS argues the Government document fails to recognise the profound difference between special schools and units and mainstream schools. Classes are small in special schools but far larger in mainstream classes where SEN pupils are often integrated. It will therefore be impossible to prepare individualised learning programmes.
The union adds: "The notion of an 80 per cent benchmark for individual pupils attaining their IEP targets will produce pressure on schools to lower targets. This is not unlike the situation in regard to attendance targets. The objectivity in this process is likely to approximate to nil".
The EIS has also asked members to be vigilant in ensuring classroom assistants to do not usurp the role of teachers. Fred Forrester, depute general secretary, said teachers welcomed "with open arms" measures to remove non-teaching duties but cautioned that the presence of other adults was irrelevant to class size.
Assistants could support literacy by reading or telling stories but assessment of reading was a professional task that must be carried out by the teacher. The union wants Government guidelines to be applied consistently across Scotland.