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Why Your Goods Get Stuck at Kenyan Ports and How to Avoid Delays

September 24, 2025 by
Valarie Waswa

If you have ever tried to import or export goods through Kenya’s ports, you know how stressful the process can be. One mistake in your paperwork and your shipment sits in a container yard racking up storage fees. Every extra day means money lost, frustrated clients, and sometimes goods that spoil before they even reach the shelves. The good news is that most delays come from a handful of avoidable mistakes. Let’s look at what usually goes wrong and how you can keep your goods moving.

Why Port Delays Matter

Delays at the port can drain your profits fast. Importers often face demurrage fees for containers that overstay at the port. Missed delivery dates damage business relationships and hurt your reputation. In some cases, regulators even seize goods if compliance gaps are serious enough. The financial and reputational damage can be severe, especially for small and mid-sized businesses.

Common Compliance Mistakes

  1. Wrong HS Codes

Every product must be classified using a Harmonized System (HS) code. Get it wrong, and customs will flag your shipment for reassessment. That means delays, extra taxes, and penalties.

2. Missing Permits and Licenses

Certain goods like food, pharmaceuticals, or chemicals require specific permits before import. If you don’t secure them early, your goods will not clear. Customs does not bend on this.

3. Incomplete or Mismatched Documentation

Your invoice, packing list, and bill of lading must match perfectly. Even small errors, like a wrong weight or inconsistent item description, can cause your goods to be held for verification.

4. Outdated KRA or EPZA Registration

Businesses must keep their tax and customs registration updated. Outdated or incomplete details can block clearance until you fix them.

5. Missing Certificates

Some goods require health, safety, or conformity certificates. If you do not provide them upfront, expect long delays and added inspection costs.

6. Mis-declared Value or Origin

Undervaluing goods or mis-stating the country of origin often leads to investigations. Customs takes these cases seriously and can impose stiff penalties.

7. Poor Shipping Instructions

Using the wrong International Commercial terms (incoterms) or failing to set clear shipping terms with your supplier leads to confusion about who is responsible for clearance. That confusion often translates to delays.

8. Weak Oversight of Customs Agents

Your customs agent is only as good as the instructions you give them. Poor oversight leads to mistakes in declarations that you, not the agent, ultimately pay for.


A Real-World Example

One client recently imported machinery for a construction project. Their packing list described the goods differently from the commercial invoice. Customs flagged the shipment, and the container sat idle for almost three weeks. By the time the goods were cleared, the client had paid more than KES 800,000 in extra storage and demurrage charges. A simple pre-shipment review could have prevented the entire problem.

How to Prevent Delays

Most clearance problems are avoidable if you prepare well. Here’s how:

  1. Verify HS Codes Early

Every product has a specific Harmonized System (HS) code that determines duty and tax rates. Misclassification leads to disputes, extra costs, and sometimes seizure. Confirm the right codes with your supplier and a trusted clearing agent before the goods even leave origin.

2. Secure Permits and Certificates in Advance

Don’t wait until your cargo is already at the port to apply for regulatory approvals. Whether it’s KEBS certification, health permits, or phytosanitary documents, get them sorted before shipping. Missing paperwork is one of the top reasons shipments sit in port warehouses for weeks.

3. Standardize Invoices and Packing Lists

KRA officers look closely at documents. If your invoice shows one figure and your packing list another, expect delays. Use consistent formats and double-check quantities, weights, and descriptions. Clear documentation makes your goods move faster.

4. Choose and Monitor Your Clearing Agent

Your customs agent can either smoothen or complicate the process. Work with licensed, reputable agents who know Kenya’s systems. Still, don’t disappear once you hire them. Stay involved, ask for updates, and ensure they act in your best interest.

5. Keep Your Business Records Current

KRA pin issues or expired registrations can freeze clearance instantly. Make sure your tax filings, company registration, and licenses are current. This way, you avoid unnecessary red flags during the clearance process.


When You Need Legal Help

Sometimes compliance issues go beyond checklists. You need legal support when customs disputes escalate, when valuation challenges arise, or when goods are seized. You also need guidance on contracts with suppliers, risk allocation in shipping, and compliance systems for regular import and export operations. That is where a law firm like ours comes in.


How We Support Clients

We know that every shipment is different, so we adapt our legal and compliance support to your business needs.

  1. Pre-Shipment Compliance Audits

We review your paperwork, contracts, and regulatory requirements before your cargo leaves origin. This prevents surprises at the port and keeps your clearance smooth.

2. Contract and Incoterm Review

The wrong contract clause or poorly defined Incoterms can shift risk and costs onto you. We help draft and negotiate terms that protect your interests from supplier to final delivery.

3. Direct Liaison with Authorities

We engage with KRA, customs officers, and regulators on your behalf to resolve bottlenecks quickly and professionally, reducing costly delays.

4. Permit and Certificate Support

From KEBS to health and phytosanitary approvals, we guide you through applications and submissions so that all documents are in place before your goods arrive.

5. Customs Dispute Resolution

If disputes arise over valuation, classification, or seizures, we step in to negotiate, file appeals, or secure fair settlements.

6. Ongoing Retainer Support

For regular importers and exporters, we provide monthly retainers covering continuous advisory, compliance monitoring, and quick response to emerging issues.


Take the Next Step

Don’t wait until your shipment is stuck in Mombasa or JKIA to look for help. The earlier you act, the smoother your goods will move. Book a consultation today and get our Pre-Shipment Compliance Checklist that will help you avoid the common mistakes that cost Kenyan businesses millions each year.


About the Author

Valarie Waswa is a lawyer by profession, an Advocate of the High Court of Kenya and East Africa by extension, and the Founding Partner of Valarie Waswa & Co. Advocates


Contact Us

For more information, contact us on WhatsApp Business at +254 707 059 485 or email us at info@valariewaswa.com