The military said the drone had flown from Israeli territory and was subsequently targeted by an Israeli warplane in southern Gaza.
"Recently, several attempts to smuggle weapons into the Gaza Strip using drones have been detected," the military said in a statement.
"The IDF (military) struck the drone in southern Gaza, along with two additional suspects who were collecting it," it said, without specifying their fate.
The Israeli military has previously said it thwarted similar attempts to smuggle weapons using drones.
On Sunday, it identified a drone crossing from Egypt in to Israeli territory.
"Following pursuit in the area the weapons smuggling was thwarted by the forces," it said at the time.
It was unclear whether Wednesday's strike was the first the military conducted in Gaza since the ongoing 42-day phase of a ceasefire took effect on January 19.
Israel and Hamas agreed to a truce following negotiations mediated by Qatar, Egypt and the United States.
Since the truce began, both sides have carried out five hostage-prisoner exchanges, with Hamas releasing 16 Israeli hostages in exchange for hundreds of Palestinian prisoners freed from Israeli jails.
However, the ceasefire is under increasing strain after Israel threatened to resume fighting if Hamas does not hand over more hostages by this weekend.
Hamas, while reaffirming its commitment to the truce, has accused Israel of violations.
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