The shakes may have been tainted with bleach, according to a statement from the NYC Police Benevolent Association.
The NYPD launched an investigation after the officers fell ill and determined early Tuesday morning that there was no criminality by employees, according to a tweet from NYPD Detective Chief Rodney Harrison.
Investigators believe a cleaning solution used to clean the milkshake machines wasn't fully cleared and may have gotten into the officers' drinks.
The officers bought the beverages at the restaurant chain's lower Manhattan location around 8:30 p.m., a spokeswoman for the department said.
All three officers were transported to a local hospital where they were treated, observed and released, according to the spokeswoman.
The NYCPBA, which represents more than 50,000 active and retired police officers, said in a statement posted to Twitter Monday night that the officers "discovered that a toxic substance, believed to be bleach, had been placed in their beverages."
The officers had already ingested part of the beverages when they noticed a substance was in their drinks, the statement said.
"When NYC police officers cannot even take meal without coming under attack, it is clear that environment in which we work has deteriorated to a critical level," PBA President Patrick Lynch wrote.
Shake Shack said in a tweet Monday night they were "horrified by the reports of officers injured," and were working with police on investigation.
In an update tweet Tuesday morning the burger chain said they were "relieved to hear the officers are all okay" and are "working hard to get the full picture."
CNN has reached out for further comment from the restaurant but has not yet heard back.
CNN's Brynn Gingras contributed to this report.