The Service & Food Workers Union believes Dunedin and Wakari Hospitals have had systemic cleaning issues for many years.
Both hospitals are dealing with an outbreak of norovirus.
The uon says there is a sense among some cleaners at the hospital that they are not contracted for enough hours to complete their cleaning to the highest standard.
It believes cleaning services should be part of the core function of a hospital and not contracted out. It wants the Otago District Health Board to review the situation.
Four wards at Dunedin Hospital are closed because of norovirus. Twenty-two patients were in isolation on Wednesday.
Visiting restrictions remain in place at both hospitals. Altogether, more than 120 staff and patients are affected.