Berths 3A, 3B, 3E and 3W will be solely used for 0.5pc sulphur marine fuels.
The date for the transition to the new berth configuration will depend on market demand, and future changes to the infrastructure may be required nearer 2020, the port said in a letter to bunker market participants.
The IMO rules, which cap global sulphur content in bunker fuels at 0.5pc, come into effect on 1 January, 2020. By allocating these dedicated berths, the port aims to ensure sufficient infrastructure is available to handle various grades of IMO-compliant marine fuels to minimise vessel delays and to maintain product integrity.
"There remains a lot of uncertainty and the lack of clarity about market fundamentals, like, supply, demand, product availability and pricing, which means a flexible approach to the segregation of products is required," the port said.
Fujairah is the Middle East's largest bunkering hub. It is likely to have different 0.5pc fuel oil grades, marine gasoil (MGO) and high-sulphur fuel oil (HSFO) available when the IMO cap comes into force.