The incidents have prompted fears people could be unknowingly taking eutylone, a stimulant in the synthetic cathinone family.
According to volunteer testing organisation Know Your Stuff NZ, it is impossible to tell the difference between MDMA and eutylone on smell or sight alone.
A risk with eutylone was that people would believe the drug had not worked and take another pill, leading to side effects such as sleeplessness, stomach upsets and paranoia. In extreme cases it could cause seizures and death.
McKee was concerned about the effects such a drug could have on Wellingtonians, particularly as students and young people returned to the city after the summer break.
"We don't want somebody falling over or dying this weekend after taking those pills," he said.
"They don't know actually what they're taking and the damage that it can cause.
"There's obviously some form of drug, potentially [eutylone] that's in the city and being sold... to our young people, and we know they're taking them thinking they're going to be taking ecstasy. Potentially they are causing themselves some significant harm or damage to their bodies with this drug that they're taking."
He called for partygoers to be "vigilant", and asked friends to think about intervening if they noticed their mates were contemplating taking pills.
"We want our people to enjoy the city and have a good time and be safe. It's a vibrant city but just be conscious and aware of these pills that are actually not what people think they are."