Deloitte & Touche, the firm's administrator, has gradually closed or sold off parts of the business since it was put into administration last month.
The Tower Hamlets schools PFI contract, worth £88.5m, was the largest of Ballast's five remaining facilities management contracts.
A spokesperson for Tower Hamlets council said: "Ballast has issued redundancy notices to people on site. Maintenance work with other contractors is still continuing."
The project is being run by a consortium led by investment bank Babcock & Brown. Babcock terminated the FM contract because of concerns over Ballast's future. The consultant has since taken on some of Ballast's staff.
A source close to Ballast said: "It was a juicy contract – we were talking about 27 schools over a 25-year period."
Deloitte & Touche has also terminated the contract of Phillip Cooper, the former managing director of Ballast's PFI and FM division. However, Cooper is being kept on in an advisory role while the administrator attempts to collect the £2m that Ballast is owed for work on PFI and FM schemes.
Subcontractors owed money continue to pool resources in their fight for payment. The latest group comprises at least five Scottish companies owed more than £5m.
The firms are seeking talks with their employer, Innovate East Lothian, the consortium containing Ballast that is running the East Lothian schools PPP.
The Scottish group said that up to 1000 jobs across the five companies could be at risk. A spokesperson for the subcontractors said: "Innovate must accept responsibility on this matter. We must not be hung out to dry on this project."