The Kenya Ports Authority is seeking to reduce the number of agencies operating within the Customs points to five from 51, as part of efforts to streamline operations.
"Except the Kenya Revenue Authority, every other agency must be outside the port, and this is best practice. We hope that we will push this proposal through so that we are not liable for congestion and other issues," said KPA managing director Dr Daniel Manduku.
He said that some of the duties performed by agencies operating within the port overlapped.
The announcement comes after Uganda, Rwanda, South Sudan and Burundi, which use the port of Mombasa, complained of inefficiencies and delays in clearing of goods, adding to the cost of doing business.
The EAC partner states want the state agencies kicked out of the Customs units at the ports and border points.
Cabinet Secretary for EAC and Regional Development Adan Mohamed said that only four "critical" certification bodies should remain at the port of Mombasa, the Nairobi Inland Container Depot and at airports and border points.
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They are the KPA, Kenya Revenue Authority, Kenya Bureau of Standards, and the Kenya Railways Corporation.
However, the proposal has elicited mixed reactions with a section of stakeholders asking KPA to first boost efficiency.
The chief executive of the Container Freight Stations Association Daniel Nzeki said the plan to eject agencies from the port will improve efficiency and trade.
But the Kenya International Freight and Warehousing Association national chairman William Ojonyo said that while the proposal is a step in the right direction, it can be upscaled.
"The people who delay our cargo are KRA, KPA itself, Kebs and the clearing agencies; they need to streamline their operations," he said.
The Kenya Ship Agents Association also called for streamlining of the documentation processes.
"Without these improvements there will still be bottlenecks. For example when cargo is imported into the country, a certificate of conformity is issued at the loading port.
"But again Kebs takes samples from the cargo when it reaches the port and by the time results are out, a number of days are gone and we incur extra charges," said the association's assistant executive officer Aziza Mwanthi.
But the Car Importers Association of Kenya said the removal of the agencies from the port will only add to the delays in clearing cargo.
"At the end of the day you still need these agencies. Ejecting them will mean going to find them at their new location," said the association's chairman Peter Otieno. "It would be better to move them to a central place."