The men were stationed at Linton Military Camp - the largest New Zealand army base, located just south of Palmerston North.
A New Zealand Defence Force spokeswoman told NZME News Service "several soldiers" were taken into custody by police. An investigation was now underway.
"Any charges laid before the courts will be at the discretion of the New Zealand Police. No further comment will be made by the NZDF," the spokeswoman said.
Police Senior Sergeant Steve Crawford said the incident was a "timely reminder" taking unknown substances was a serious risk.
"This is a timely reminder to people of the dangers of taking substances where they don't know the source.
"If you are taking a substance that you don't know where it is from or what it contains, you are taking very serious risks with your health and you are putting your life at risk."
Inquiries regarding the substance and its source were continuing, police said.
A source said the substance was thought to be "N-bomb" - the illegal synthetic drug 25B-NBOMe, which is a powerful synthetic hallucinogen related to amphetamines.
Earlier this month, the newly emerged drug led to six people being treated in Christchurch Hospital.
One of the patients, a 20-year-old man, was on life support in a critical condition in intensive care for a number of days after suffering multiple organ failure.
A Christchurch Hospital spokeswoman said last week the man was in a stable condition but told NZME News Service today an immediate update could not be released without family permission.
Police and health officials are warning people to avoid any drug that is sold as NBOMe or an 'LSD-type drug' and seek medical help immediately for anyone suffering from adverse reactions.
The drug is sold as a white powder or in capsules and has been related to deaths in Australia and Asia.
Canterbury Senior Sergeant Jason Stewart said officers were working closely with Customs and other agencies nationwide to target users and distributors of synthetic substances.
"In the case of synthetics users have very little knowledge of what they are actually taking and the public to be aware that there is a very real risk of serious harm or fatalities when people abuse any form of drug," Mr Stewart said.
Canterbury emergency medicine specialist Dr Paul Gee said it was a powerful synthetic hallucinogen.
"Hallucinations , confusion and agitation are common symptoms, sometimes leading to uncontrollable violent behaviour.
"Recreational doses are measured in tiny microgram quantities (less than the size of a match-head) so it is very easy to use more than intended," Dr Gee said.
