Tony Blair and Lord Sainsbury, science minister, announced last April that the Department for Trade and Industry would provide around pound;250 million - pound;750,000 per school - to rebuild or refurbish the labs.
Lord Sainsbury said the money was needed urgently because science facilities in a third of all secondary schools were "appallingly out of date".
However, the Labour peer has now indicated it may take another 15 years before the work is done in many schools and there may be no DTI funding.
The Association for School and College Leaders wrote to him asking what was happening. In reply, Lord Sainsbury said the DTI was waiting to see what the Department for Education and Skills would do.
He said the Treasury had already allocated the "substantial sum" of pound;17.5 billion for the DfES Building Schools for the Future programme, which will rebuild or refurbish all secondary schools by 2020.
Lord Sainsbury said: "This programme includes commitments to build or modernise all secondary science laboratories over the next 10 to 15 years.
"We will be working together to assess whether Building Schools for the Future will be able to fulfill this commitment and whether we need to make a further bid to increase resources."
The Prime Minister and Ruth Kelly, the Education Secretary, stressed the importance of new laboratories when they made the pledge three weeks before the general election.
Ms Kelly said: "To find the next generation of leading scientists we need to get kids excited, studying in the highest quality, most modern facilities."
John Dunford, general secretary of the ASCL, said dropping the pledge would make schools more cynical about the promises of politicians.
"Schools will be extremely frustrated and disappointed to find this was election smoke and mirrors," he said.
Derek Bell, chief executive of the Association for Science Education, said science teachers would be unhappy if they had to wait more than a decade for new laboratories, as it was more difficult to do practical work in older facilities.
Pupils at Pershore high school, Worcestershire, have shown increased interest in science since it replaced its 35-year-old laboratories with a pound;3.1m science block last year.
Stuart Arch, head of science, said students had been relieved to leave behind the school's old, cramped laboratories with leaking sinks and damaged floors for larger high-tech rooms with moveable desks and computer projectors.
"We have to make the subject relevant and exciting - and that is bound to be easier if you have new facilities instead of a laboratory from the 1960s," said Mr Arch.
A DTI spokeswoman said further announcements on school laboratories would be made "in due course".