The Environment Agency warned on Sunday the site could become flooded due to rising water levels on the River Thames between Newbridge and Kings Lock.
At a special council meeting of the Liberal Democrat cabinet, councillors agreed the secondary school would be on a temporary site in a building previously used by the Environment Agency and Defra on Burghill Road, Brentry, for one year.
However, they suggested that conditions be added in an effort to minimise the impact on the environment and people living near the site.
The Department of Environment, Food and Agriculture is making checks on each site planted since 2007.
"Flood defences are now in operation and the situation on site is being constantly monitored, " said an Environment Agency spokesperson.
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Opponents are concerned about the impact the site's expansion could have on their health and the environment.
Developer FCC Environment proposed building a facility to turn vegetation into electricity on land at Sutton Courtenay landfill site.
The Environment Agency said a flood alert remained in place and pumps and officers would remain on site working to ease the situation.
The Environment Agency is already investigating how water from the river Clwyd breached flood defences built on the Glasdir site.
The Environment Agency said it had been made aware on Thursday of an additional seat of fire on the same site, which is being managed as a controlled burn.
Protestors had called on UK Environment Minister Mr Meacher to halt the trials after he questioned the location of a GM test site in Warwickshire.
They are seeking a judicial review into why the Department of the Environment did not request more information on the impact the development would have on newts, bats and badgers at the site.
"This is because a substantial quantity of potentially explosive pharmaceutical material - Isosorbide Dinitrate (ISDN Pure) - has been identified on the site following a recent joint inspection by the Health and Safety Executive (HSE) and Environment Agency Wales, " explained the council officer.
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In a statement, the council's chief executive, Colin Everett, said "a substantial quantity of potentially explosive pharmaceutical material - Isosorbide Dinitrate (ISDN Pure) - has been identified on the site following a recent joint inspection by the Health and Safety Executive (HSE) and Environment Agency Wales".
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The Environment Agency served an enforcement notice on the owners before the fire to restrict the levels of wood being brought onto the site.
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