Croydon Council has failed to secure the £350million in government funding it needs to transform secondary schools in the borough.
The council’s bid was rejected in favour of other councils who were deemed more ready to deliver their plans.
All local authorities who apply for BSF funding will be admitted into the scheme.
They have to show they are ready to deliver their plans straight away.
In December the Croydon Guardian revealed the council had yet to secure the funds it needed to begin the ambitious changes planned for local schools.
Croydon were expecting to be among the latest tranche of authorities admitted into the programme last week.
However, their plans were not deemed ready enough.
A spokeswoman from Partnership for Schools said: “They were unsuccessful at this time, hopefully they will resubmit their plans in three months time.
“There were a lot of local authorities in that group. Other local authorities were more ready to start.
“We expect Croydon to join shortly.”
How much of a delay this set back will cause has yet to be determined.
In June last year, the council announced its controversial plans for the transformation of secondary school education.
Building was due to begin in 2012.
The plans included three new academies and sponsors have been announced for Ashburton Community School, Selsdon High School and Haling Manor.
There are due to be two London Challenge Trust schools at Addington High School and Westwood Language College.
Most schools will gain a sixth form and there will be special education provided for children with learning difficulties.
Many schools are due to receive brand new buildings and facilities depending on their needs.
Dave Hill, executive director, children, young people and learners at Croydon Council said: “Croydon and Kingston were two of only nine local authorities across the whole country invited by Partnership for Schools to submit preparation documents for inclusion in the initial wave of this BSF programme.
"PfS has announced that each wave of the programme will include six local authorities so we are therefore fully confident of being included in the next wave.
"This decision will have absolutely no bearing on our BSF timescale.”