Three French chefs won individual honors, with Alain Passard of Arpege given a lifetime achievement award, French-born Dominique Crenn named best female chef and Pierre Herme best pastry chef.
Italy's "Osteria Francescana" was crowned world's best restaurant of 2016.
The rest of the top 50 saw France featured at sixth place with Mirazur in Menton, at 19th with the Arpege in Paris, and managed to sneak in at 50th with the Septime in Paris.
The accolades came after critics complained last year that the system was open to abuse since the jury do not have to offer physical evidence of having actually visited any particular restaurant.
The bulk of those complaints came from France, which in 2016 made it into the top ten for the first time in three years but has never managed to win first prize.
The 2016 list included restaurants in 23 countries on six continents -- but half were in Europe. Asia and the United States each had six in the top 50, while South America and Scandinavia each had five.
Spain had seven restaurants on the list, including three in the top 10.
The awards, run by trade magazine Restaurant, began in 2002 and have become a reference for the world's foodies, but were hit last year by allegations of cosy deals between restaurants and jury members.
The contest is run by British media company William Reed, and criticism has focused on the methodology used to select the best restaurants.
Its jury is made up of 972 experts, including food writers, chefs, restaurant owners and gourmets. Members list their choices in order of preference, based on where they have eaten in the past 18 months.
There is no pre-determined checklist of criteria, but there are strict voting rules.
In the face of complaints, the organizers say consultancy firm Deloitte oversees voting, to ensure the "integrity and authenticity" of the process.