The problem cropped up with uncertainty over the future of the sole onshore fuel storage facility, which is being returned on a court order to the port by Lanka Marine Services (LMS), a unit of the John Keells Holdings group.
JKH said earlier it would shift remaining stocks in the tanks to barges and asked time from court until September 10 to do so.
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The port has decided to open the use of the tanks to all licensed bunker suppliers
Other suppliers now use tanker barges to store and supply bunker or ship fuels.
"There's going to be a shortage of bunkers in Colombo," one supplier said. "We're still not allowed to store the oil in the onshore tanks and our stocks have finished.
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Fresh stocks are scheduled to arrive around September 14.
Most of the ship fuel delivered in Colombo is imported and the sole refinery operated by the state-owned Ceylon Petrole