The allegations were made by Ian Charlesworth, director of special projects (competition strategy), who represented himself at industrial tribunal.
Mr Charlesworth said his union, the GMB, was last week considering whether or not to pursue his claims, either by appealing the tribunal's judgment or by bringing a new claim of breach of contract. He said he would not return to tribunal without representation.
His claims against the council and his chief executive were the latest development in a long running case which has involved senior officers and councillors, and allegations of fraud in the council's now disbanded direct labour organisation, Bradmet.
Mr Charlesworth was pressing to conduct his own investigation into losses incurred by Bradmet's highways maintenance department before his suspension.
An industrial tribunal this month dismissed Mr Charlesworth's claims: 'We do not find . . . that any of them are well-founded,' it said. But the tribunal deplored the deterioration of relations between councillors and senior officers.
The judgment expressed regret that Mr Charlesworth had allowed his 'considerable ability to be side-tracked into a pursuit of what appears to us to be an . . . unfortunate vendetta against Mr Penn and his colleagues'.
Council leader Tony Miller announced that Bradford would take into account in a current review of personnel procedures criticisms by the tribunal of its handling of complaints made by staff.
The council has been conducting an internal inquiry with the help of independent advisers into more than 70 complaints made by Mr Charlesworth about Mr Penn, corporate services director Philip Robinson, former legal services director Allen Sykes and legal services manager Gerry Danby. The policy and resources committee is to be told on Tuesday that the complaints have not been upheld.
Mr Miller said: 'The officers concerned in the complaints have been formally advised that the inquiry is satisfied that the complaints are not substantiated.'