Yes!
The recent decision notice of the ICO made against Hertfordshire County Council accepted that some of the information being requested was subject to a contractual obligation of confidence (other information was not received from a third party, so the section 41 exemption could not apply anyway). Not only that, but it had the necessary qualities of confidence (the circumstances imparted an obligation of confidence, the information was not trivial and was not available by other means). But even so, the section 41 exemption did not mean that the information should be withheld.
Why?
Because in order for a disclosure to constitute an actionable breach of confidence, the common law of confidence requires that there is not a defence that the disclosure was in the public interest. In this case the ICO considered that it was in the public interest to disclose how the Council was investing taxpayers’ money, and therefore there would have been no breach of that obligation.
Lesson: just because you have a confidentiality provision in your contract with a public authority does not mean that it will escape disclosure under FOIA. You need to be really sure that the information truly is confidential, and that there is no overriding public interest requiring its disclosure. Moreover, you must be aware that the only information protected is that moving from the private company to the public authority - the contract itself, information developed by both parties and information provided by the public authority will not benefit from the exemption.