"We know of deaths of terrorists in military detention centres and they are under investigation," a spokesman told AFP.
The army did not provide details regarding how many detainees had died or the circumstances of their deaths.
Hundreds of Palestinians are being held in detention centres in southern Israel, having been detained in military operations across Gaza since the war erupted on October 7.
On Tuesday Israeli newspaper Haaretz reported that "several of them have died" in these detention facilities.
The report said the prisoners died at the Sde Teiman base near the city of Beersheva.
The detainees held at this facility are "blindfolded and handcuffed for most of the day and the lights are on at the facility throughout the night", the report said.
The detainees had been "involved in terrorist activities", said the spokesman.
"Prisoners deemed not involved in terrorist activities are sent back to Gaza Strip," he added.
Last week the army received condemnation after Israeli television showed scores of stripped Palestinian men sitting on a Gaza street in military custody.
One clip showed the arm of a soldier in the foreground, suggesting it was filmed by a member of the military.
In another clip, a group of blindfolded men are seen sitting with their hands tied behind their backs as Israeli soldiers watch them.
Earlier this month the army announced that more than "500 terrorists" had been arrested in Gaza.
The war between Israel and Hamas, which rules the Gaza Strip, began after the Islamist group carried out a bloody attack on southern Israel on October 7 which killed around 1,140 people, according to an AFP tally based on the latest official Israeli figures.
Israeli's ensuing military campaign in Gaza has so far killed at least 19,667 people, according to the territory's health ministry.
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