Zulkifli visited the restaurant Wednesday and ordered it to be shut down, The Jakarta Post's Bali Daily reported.
The dolphins at the floating restaurant will be relocated to the Dolphin Rehabilitation Center in Kemujan, Karimun Jawa.
"We will release them back into their natural habitat but we have to complete some observations before doing so," Zulkifli said.
The Akame Dolphin Bay Restaurant is shaped like a ship and has a 1,400 square-foot pool in the middle where dolphins perform daily.
"This environment is not suitable for dolphins. Wild life will be better for them," Zulkifli said.
Zulkifli acknowledged the restaurant has proper permits to run a dolphin attraction, but that public outcry prompted the closure of the attraction.
"The existing rule actually gives permission for these kind of activities. But I understand that many people have criticized this sort of activity. Many people have protested via Twitter. This attraction received the attention of the international community. Therefore, we believe that it should be stopped," he stressed.
The forestry minister also pledged to shut down other such attractions.
"We will do the same thing in other places," he said.