In an attempt to prevent paparazzi from using unmanned drones from filming the event, Refaeli and Ezra wanted the airspace over the venue to be shut down.
The wedding is taking place in a heavily secured establishment in the northern Israeli Carmel Forest, near the port of Haifa.
The airspace request created a standoff between the Transportation Ministry and Civil Aviation Authority.
Transportation Minister Israel Katz ordered the aviation authority to immediately cancel a flight prohibition in the skies above the wedding.
Katz then threatened to sack the aviation authority’s boss when his instructions were not immediately followed.
“If the skies above Refaeli’s wedding won’t be open, you will be transferred from your position,” the minister wrote in a letter, Channel 10 television reported.
“The skies belong to the entire public and no monopoly should be granted to anyone for commercial reasons,” the letter read.
Some 600 guests are expected to attend the high-society wedding, but other details are being kept under wraps.
This is the second marriage for the 30-year-old model, who first got married at 18.
Ezra, who is 10 years her senior, belongs to one of the wealthiest families in Israel which imports food products and whose fortune is estimated at 400 million shekels (100 million dollars).
Refaeli was initially known internationally when she was dating Hollywood star Leonardo DiCaprio. The couple split in 2011.
She did her first modelling campaign as an 8-month-old. Her big breakthrough was in 2007, when she became the first Israeli model to make it to the cover of Sports Illustrated.
Today Refaeli hosts Israel’s version of the reality show, X-Factor, and is part owner of Carolina Lemke Berlin eyeglasses and Urbanica, a chain for affordable fashion.
She told the September edition of the Israeli magazine At (You) that she hopes to get pregnant soon, saying “I’m ready to be a mother.”