Many drug users have unknowingly ingested a potentially deadly batch of fentanyl circulating in Sydney, health authorities warn.

NSW Health issued an alert on Sunday after a number of individuals who believed they were using cocaine or other stimulants unwittingly took the synthetic opioid acetyl-fentanyl.

Drug users in Sydney are mistakenly using fentanyl instead of cocaine as the two are indistinguishable.

These people became severely unwell, developing toxicity from the illicit substance, Andrew Dawson at the NSW Poisons Information Centre said.

"We’ve seen several people recently where acetyl-fentanyl was taken unknowingly and was associated with serious harm," Professor Dawson said.