The statement on Sunday from Prime Minister Benjamin Netanyahu's office said Israel "will act with all means to seek justice with the criminals responsible for his death".
Zvi Kogan went missing on Thursday and there were suspicions he had been kidnapped.
The Prime Minister's Office and the Ministry of Foreign Affairs:— Prime Minister of Israel (@IsraeliPM) The UAE intelligence and security authorities have located the body of Zvi Kogan, who has been missing since Thursday, 21 November 2024.November 24, 2024
His disappearance comes as Iran has been threatening to retaliate against Israel after the two countries traded fire in October.
The Emirati government has not acknowledged that Kogan had been found dead.
Kogan's wife, Rivky, is a US citizen who lived with him in the UAE.
She is the niece of Rabbi Gavriel Holtzberg, who was killed in the 2008 Mumbai attacks.
The Chabad Lubavitch movement, a prominent and highly observant branch of Orthodox Judaism, said Kogan was last seen in Dubai.
A video circulating on social media showed him earlier in the week at a Kosher grocery store in the city-state.
The Rimon Market, a Kosher grocery store that he managed on Dubai's busy Al Wasl Road, was shut on Sunday.
The Chabad Lubavitch movement also described Kogan as being an emissary of the branch, which is based in Brooklyn's Crown Heights neighbourhood in New York.
Early on Sunday, the UAE's state-run WAM news agency acknowledged Kogan's disappearance but pointedly did not acknowledge he held Israeli citizenship, referring to him only as being Moldovan.
The Emirati Interior Ministry described Kogan as being "missing and out of contact".
"Specialised authorities immediately began search and investigation operations upon receiving the report," it said.
Rabbi Zvi Kogan managed The Rimon Market, a Kosher grocery store on Dubai's busy Al Wasl Road. (AP PHOTO)
The UAE is an autocratic federation of seven sheikhdoms on the Arabian Peninsula and is also home to Abu Dhabi.
Local Jewish officials in the UAE declined to comment.
While the Israeli statement did not mention Iran, Iranian intelligence services have carried out past kidnappings in the UAE.
Western officials believe Iran runs intelligence operations in the UAE and keeps tabs on the hundreds of thousands of Iranians living across the country.
Iran is suspected of kidnapping and later killing British Iranian national Abbas Yazdi in Dubai in 2013, although Tehran has denied involvement.
Iran also kidnapped Iranian German national Jamshid Sharmahd from Dubai in 2020, taking him back to Tehran, where he was executed in October.
The UAE diplomatically recognised Israel in 2020.
Since then, Israelis have come to the UAE to set up businesses and vacation.
Emirati airlines have been a key link for Israel to the rest of the world as other carriers have stopped flying to Ben Gurion International Airport in Tel Aviv amid the wars.
The UAE also has a burgeoning Jewish community, with synagogues and businesses catering to kosher diners.
However, the Mideast wars have sparked deep anger among Emiratis, Arab nationals from other states and others living in the UAE.
