Ichikidana restaurant, located in the capital's Mahane Yehuda Market, decided to waive the certification after Shmuel Zamelman, the market's new kashrut supervisor, began forcing restaurants to buy their vegetables in specific stores.
A letter posted on Facebook by the restaurant owners received many shares and positive comments.
Ichikidana owner, Lehava Silman Herman, explained: "We are a vegan restaurant, so the kashrut is irrelevant, but we decided to cooperate with the Rabbinate because of religious Jews.
"After (Zamelman) arrived and decided that we must only buy in certain stores, I decided that I would not cooperate any longer," she said.
The Rabbinate issued the following statement in response: "Every restaurant which receives a kosher certification must take leaves and vegetables from a supervised place only. This has been a Rabbinate order for the past 30 years. The Rabbinate does not profit from this arrangement."