John Mitchell, president of the Headteachers' Association of Scotland, warned: "Schools all over Scotland will need to search to find replacement agencies to take on the valuable work undertaken by the centre. Any replacements are likely to be much more expensive and are unlikely to be willing to share information freely among all Scottish schools. None will be able to cover all of the services the centre currently provides."
The former regional authorities provided pound;200,000 a year to subsidise the centre but the company that runs it has ceased trading after 30 years because it has been unable to obtain firm guarantees of support from the new councils.
David Standley, deputy rector at Edinburgh Academy and immediate past president of the Association for Science Education, has already written to school science departments urging them to enlist the support of heads in campaigning to save the centre.
Mr Mitchell said: "I hope emergency action can be taken to keep the centre going until the new authorities have time to fully consider the consequences of losing such a valuable resource. Once destroyed, it will be impossible to start again."