Red items were typically high in sugar, salt, fat, were solid in large portion sizes, or were carbonated or sugary drinks.
The audit report recommended they should be removed completely, or substituted with a healthier option.
There are five food outlets on SDHB premises: Showline cafe at Wakari, Revive, The Dispensary and Antidote in Dunedin Hospital, and Om Nom Nom at Southland Hospital.
The SDHB did not not identify which cafe achieved a pass grade.
Having previously banned sugar-sweetened drinks, in 2018 the SDHB introduced a new healthier food and beverage options policy at all SDHB hospitals and facilities.
The changes were in line with the Ministry of Health's national healthy food and drink policy, with which all DHBs are obliged to comply.
The changes meant cafe operators had had to alter some ingredients and reduce some portion sizes.
The report commended cafe operators for their efforts in making changes so far, and said simple changes such as displaying more green than amber items, substituting white varieties of pasta and rice for wholemeal or brown varieties, and ensuring more vegetarian options were available would help cafes better meet the policy recommendations.
The report said SDHB-based cafes should role-model healthy food and drink environments to the community.