Mr Prendergast said antibiotic waste in the environment should also be limited because it can cause resistance to the drugs.
Pharmaceutical waste is being looked at by regional councils around the country as an "emerging contaminant", said Juliet Milne, aquatic ecosystems team leader at GWRC.
"But there are very few laboratories in New Zealand that have the technology to test these sorts of contaminants, particularly at the low levels in which they tend to be found in waterways."
The testing is also costly.
The ministry has recommended Masterton and South Wairarapa district councils prohibit cytotoxic waste and limit pharmaceutical waste under their shared trade waste bylaw, now being reviewed.
The bylaw would limit the volume and concentration of pharmaceutical waste being discharged into the water system. It may not have much effect on what Wairarapa pharmacies do with old and unused medicines as many have an arrangement with the district health board to collect pharmaceutical waste.
Hamish Duncan, of Duncan's Pharmacy, Masterton, said the DHB collects pharmaceutical waste from the store monthly.
Pharmacies encourage people to bring unused or old medicine back so they can safely dispose of it.
Medical waste disposal companies are usually contracted to DHBs to incinerate cytotoxic waste.
The Ministry of Business, Innovation and Employment's guidelines for cytotoxic drugs say there has been increasing concern among healthcare workers about exposure to the drugs during administration and disposal.
It says waste with low concentrations of cytotoxic wastes, for example urine, may be disposed of safely in the normal sewage system.
Ms Milne said the regional council and other councils are maintaining a "watching brief" over pharmaceuticals. It may look to include them in future monitoring programmes.
The council tests waterways for contaminants, including nitrogen and phosphorus, E. coli and, in urban areas, copper and zinc.
About 80 per cent of hazardous wastes in New Zealand are liquid wastes and much of this is processed through the wastewater system of sewers and wastewater treatment plants.
In New Zealand domestic wastewater is discharged into the environment at a rate of about 1.5 billion litres a day.