The federation investigated Hertfordshire University under the Freedom of Information (FOI) act after its members complained it was charging them 75 for pre-qualification questionnaires.
The university agreed to return all cheques after admitting it had "made a mistake".
"One of the main reasons behind this was to enable us to identify serious applications for the work from suitably qualified firms," said a university spokeswoman.
Salford University, also investigated by the BPIF, said it would stop charging 118 per tender once its e-procurement system was finalised.
BPIF public affairs officer Lizzy Hawkins said the news was positive but she felt concerned that the universities thought charging was a legitimate way of filtering out nuisance applications.
"We have got to keep working on this and we are encouraging people to come forward with more information on universities that are charging," said Hawkins.
"Salford said it was using the charges purely as a deterrent not to cover costs so where is the money going?"
The BPIF will continue to call on its members to report public sector procurement systems they feel are detrimental to small businesses.
It has been investigating third-party firms in charge of local authority procurement since printers raised concerns over paying up to 600 but not being guaranteed work.
BPIF vs "unfair"public sector procurement systems
- Hertfordshire University to stop charging 75 per tender
- Salford University's 118 per tender charge an "interim measure"
- Salford to launch e-tendering system as alternative
- Third party local authority suppliers should be "more accountable"
- Printers to report unfair public sector procurement systems