The ministry said: "During their stay on Malaysian soil, the passengers were not required to disembark, and after approximately five hours of waiting on the tarmac, the flight resumed its journey to Singapore."
An Emirates spokesperson said: "We regret any inconvenience caused, but the safety of our passengers is our top priority."
Malaysia has never recognised Israel, and Israeli citizens are banned from entering the country.
The Muslim-majority country is considered particularly hostile to Israel. In 2018, its then-Prime Minister, Mahathir Mohamad, labelled Jews as "hook-nosed" and condemned Israel for creating chaos in the Middle East.
In recent years, Israeli security services have uncovered various instances of Hamas terrorists receiving military training in Malaysia, often with the tacit approval of local authorities. Hamas also sends Palestinian students to Malaysia for cyber-warfare training, Israeli media reported late last year.
It comes after a commercial flight from the Seychelles to Tel Aviv carrying 128 Israelis made an unscheduled landing in Saudi Arabia.
The passengers spent one night at an airport hotel in the Red Sea port city of Jeddah in Mecca Province before being flown back to Israel the following day.
Earlier this week, a Wizz Air flight from Israel to the UK was forced to land in Serbia after a passenger attacked airline crew.
