The 57-year-old envoy, who had arrived in Israel in mid-February, was found dead in his home in Herzliya, north of the city, spokesman Micky Rosenfeld told AFP, adding that police were investigating.
Du's wife and son were not with him in Israel.
The Chinese foreign ministry said it would only comment when it had "solid" information.
Israeli police and forensics teams could be seen at the residence, a property guarded by a low wall and shaded by a leafy garden, AFP reporters said.
Du had previously served as ambassador to Ukraine, according to his biography on the embassy's website.
The Haaretz daily said initial reports said staff had found Du dead in his bed and that there were no signs of violence.
It quoted Israel's emergency medical service Magen David Adom as saying the cause of death appeared to be a cardiac incident.
A spokesman for the medical service would not provide any official information.
Du had undergone a 14-day home quarantine on arrival in Israel because of the new coronavirus outbreak, according to an interview with local media in May.
On April 2, Israel Hayom, the top-circulation Hebrew newspaper, published an editorial by Du on the theme that "Collaboration is the Cure for the Virus".
China and Israel, a strong US ally, have boosted cooperation in the high-tech and other sectors, leading Washington to urge Israel to limit Chinese investment in its strategic sectors.
Chinese embassy spokesman Wang Yongjun in a recent Jerusalem Post commentary rejected the claim and called Sino-Israeli cooperation a "win-win" situation.
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