From April 2010, all schools will be part of the UK government's Carbon Reduction Commitment (CRC) which aims to reduce carbon dioxide emissions. But while England has a raft of well-funded projects to install green technology, schools in Wales are not eligible.
Teaching unions say Wales is now lagging way behind England in funding greener schools.
The Assembly government is funding 15 school building projects through its school buildings improvement grant. To qualify, all planned buildings must be rated excellent for energy efficiency. Local authorities must also "have regard to" sustainable and energy-efficient features.
But the annual Pounds 90 million budget for the project compares poorly with the pound;21.9 billion in capital investment being spent in England over the next three years.
Dr Philip Dixon, director of the Association of Teachers and Lecturers Cymru (ATLC), said school buildings in Wales tended to be older and in a worse state of repair.
"What do we do about our school stock, a lot of which is post-war or Victorian, and which is not energy efficient?" said Dr Dixon. "Hopefully we will be lobbying the UK government for a slice of the cake."
The Assembly government said it has set a national target of reducing greenhouse gases by 3 per cent annually by 2011. According to the Welsh Local Government Association, some authorities want even higher targets. But a spokesperson for the association said: "Local government needs more support to meet these requirements."
A pledge by Jane Davidson, the former education minister, that all school buildings would be fit for purpose by 2012, was scrapped and no new target has been set.
Iwan Guy, acting director of the National Association of Head Teachers Cymru, agreed that bringing all school buildings to an acceptable standard was a huge task.
Estyn, the Welsh inspectorate, said in its 2008 report that almost half the secondaries it inspected had "some poor aspects of accommodation". Many remain badly insulated with high heating bills.
Schools can request help from a pound;2m government grant to cover energy costs over the coming year. But some have put their own money into double glazing and lower ceilings.
Dr Dixon of ATLC warns that any savings must be kept within a school's budget.