Shareholders' Council chairman Duncan Coull said despite the findings it still believed the cooperative structure was what worked best.
"Notwithstanding the findings of this report, the council remains firmly of the view that the co-operative structure is the only structure that will provide for the enduring needs of our intergenerational farming families," said in a letter prefacing the report.
Coull said it commissioned the independent report in June after criticism about Fonterra's performance from shareholders and the media.
"This work was in response to a heightened level of commentary within the supplier base, media and the broader financial community in relation to the perceived performance of our co-op since it was formed in 2001."
He said the assessment clearly showed that Fonterra's financial performance since inception had been unsatisfactory.
"When considered as a standalone investment, the average returns generated by Fonterra since inception are lower than relevant benchmarks."
The assessment looked at shareholder returns, Fonterra's return on capital and how it compares to appropriate benchmarks and segment analysis - whether Fonterra earns a higher returns on capital from its value-add business units.
Coull said the results were unambiguous and should be used to inform a wider discussion between the board, management and shareholders around the continued evolution of the co-operative.
"... and in particular what can be done to ensure ongoing returns meet, as a minimum, the opportunity cost of farmers' capital invested in the co-operative."