The organisation is calling on the Government to introduce a design "threshold" after a year-long review highlighted that the majority of schemes did not meet published criteria standards.
The £45bn BSF programme aims to rebuild or renew all of England's 3,500 secondary schools.
CABE chief executive Richard Simmons said: "What we need is a design threshold that will prevent bad schemes from continuing through the system. This would provide a very clear signal that good design is a core requirement of BSF, not an optional extra."
The review found that of the 24 schemes that are now at planning application stage, or where a single design has been chosen, only three have been rated "good" or "excellent" and 21 either "not yet good enough" or "mediocre".
Farrer Huxley principal landscape architect Noel Farrer said he agreed with the criticism and said the programme could potentially become a "gross missed opportunity".
Farrer, a CABE Enabling Panel member providing advice on the public realm and a Landscape Institute Policy Committee member, claimed the importance of the landscape was being neglected: "The benefits of quality landscape design and delivery are enormous in terms of outdoor learning spaces and vocational training resources.
"It is essential that any new schools built under BSF have a significant landscape element and that this be a requirement clearly set out. Otherwise, it will continue to represent a gross missed opportunity."