Delegates backed the EIS after Kathy Finn, a past president of the institute who spoke for the STUC's general council, infuriated the English-led NAS by claiming that a commission was unnecessary because Scottish teachers had not lost their negotiating rights and had resisted the contentious aspects of Government education policy.
"I'll tell what we want, what we really, really want and that is a Scottish parliament with powers over Scottish education and the funding of Scottish education," Ms Finn said.
John Kelly, Scottish president of the NAS, retorted that his union's demand had nothing to do with pay. Mr Kelly said: "It is a very effective negotiating body, is it not, which gives Scottish teachers less in five of the last six settlements than was imposed south of the border."
The NAS is a long-standing advocate of a pay review body which would give it more influence over salary awards.
A joint press release issued later by the NAS and the SSTA accused the EIS of having "misused its trusted position on the STUC's general council" to attack the NAS. The statement said a Scottish parliament might take five years to establish but an independent investigation into Scottish education was an immediate necessity.
In other debates at the STUC's centenary congress in Glasgow, delegates showed no intention of obliging Labour by recoiling from tax and spend motions. Demands went from investment in the early years to more support for students.
May Ferries, the EIS's president, said the #163;50 billion earmarked for Trident should fund "books not bombs". This time the institute had the NAS on its side as Mr Kelly said that Denmark spends 7.4 per cent of national wealth on education while Scotland's share is 4.9 per cent "and falling".
Stressing the importance of smaller classes in the early years of primary school, Mr Kelly said a class of 33 pupils had only seven minutes a week contact time with the teacher, the equivalent of a minute for each of the seven areas of the primary curriculum. "If they don't catch the wind at the early stages, they will never set sail."
The Government was also condemned over ministers' #163;33 million three-year package for school security. Barbara Clark, assistant general secretary of the SSTA, said a quarter of the costs would have to be met from council resources. "What resources?" she asked.
Dunblane primary would have been bottom of the list for improvement s under the criteria because it was seen as a low risk, Mrs Clark said. School security was not just about stopping "gunmen or machete maniacs or flame-throwers" but the everyday intrusions such as opportunistic theft, youths entering schools to pursue vendettas, mothers sorting out playground squabbles and even "people coming in off the street to use the toilets".