Shake Shack put out a statement saying they were "horrified" over the matter and were complying with a police investigation.
The officers were not seriously harmed but they went to the hospital for treatment.
The Detectives' Endowment Association, the labor union that represents 20,000 active and retired New York City Detectives, had earlier condemned the incident as an attack on police, claiming on Twitter that the officers were "intentionally poisoned by one or more workers".
A trio of cops getting a bad taste in their mouths after downing Shake Shack milkshakes almost became a flashpoint in the nationwide tensions between police and their communities. but cooler heads are prevailing. "In the meantime, we're relieved to hear the officers are all okay", Shale Shack said.
Among those injured was Sgt. William Maher, who was struck by an SUV and was hospitalized for several days, police said.
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"We welcome reform", Mr Shea said.
The police union, the New York City Patrolmen's Benevolent Association, said that while the officers were eating, they "discovered that a toxic substance, believed to be bleach, had been placed in their beverages". He said the officers discovered the substance and did not finish their drinks but had already ingested some of the tainted substance. "We can not afford to let our guard down for a moment".
Racial tensions in the wake of the recent deaths of George Floyd and Rayshard Brooks, among other black Americans, have renewed calls for police reforms and budget cuts nationwide.
Mr Shea said the officer was suspended without pay for discharging mace at a group of bystanders during the protests and unrest of June 1.
Shea shared a defiant message on Instagram on May 31, telling police officers that he was "extremely proud" of them as videos surfaced on social media showing them shoving protesters, yanking people's masks down to hit them with pepper spray, and even using horses and police cruisers to barrage into crowds.
NY police union President Patrick Lynch, noting that shootings and murders rose past year, said city leaders "will have to reckon with the consequences" of a strategy that de-emphasises proactive policing.