But the SLPA has told port users that it was working to solve the problems with the terminal management system and that the delays would end soon.
Shipping agents have complained to the SLPA that problems with the new computer system have resulted in reduced efficiency at the main government-run transhipment facility, the Jaya Container Terminal.
They said ships calling at Colombo face delays in getting a berth, miss connections with other vessels, or have to spend too much time at berth.
The new computerised terminal management system has been a long-felt need to modernise port operations and improve efficiency.
"There are some teething problems in the system which are causing bottlenecks," said a shipping agent.
"This has affected planning and vessel berthing.
Containers have also gone missing.
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The problems have also affected transfers of containers between different terminals in the port.
SLPA chairman Priyath Bandu Wickrama said the problems would be sorted out