Let's consider this real life example; a shipment of fresh-cut roses arrives at the port on schedule. The shipment gets flagged, but the problem isn’t the flowers, it’s the paperwork. The phytosanitary certificate lists the wrong scientific name, which is enough to trigger a hold by U.S. Customs and Border Protection (CBP) and a review by the U.S. Department of Agriculture (USDA).
While the documents are corrected and resubmitted, the roses sit. And sit. By the time the issue is resolved, the roses have started to wilt and the buyer rejects the delivery.
This happens more than you’d think. Agricultural shipments are inspected at significantly higher rates than general cargo, and perishable horticulture products operate on the tightest timelines in the supply chain. When horticulture customs clearance goes wrong, the clock keeps ticking - and the product pays the price.
Below are some of the most common customs clearance issues affecting horticulture products and what importers can do to avoid them.
The Compliance Stack for Horticulture Imports
Horticulture shipments don’t just clear customs. They have to clear multiple agencies with overlapping authority. The primary regulatory agencies are:
| Agency | Role | Common Requirements |
|---|---|---|
| Customs and Border Protection (CBP) | Entry processing; duty assessment; security screening | Commercial invoice; packing list; Importer Security Filing (ISF); entry summary |
| USDA Animal and Plant Health Inspection Service (USDA APHIS) | Plant health and pest risk management | Phytosanitary certificate; import permit (for restricted items); compliance agreement |
| U.S. Food & Drug Administration (FDA) | Food safety (if product is for human consumption) | Prior Notice; compliance with the FDA Food Safety Modernization Act (FSMA); facility registration |
| State Agriculture Departments | Additional quarantine and pest restrictions | Varies by state; may require additional certifications or inspections |
Each agency has specific documentation and inspection requirements as well as its own timeline. If any one document is incorrect, incomplete, or missing, the entire shipment gets held and perishable goods start losing value immediately. There’s no pause button on perishability.
The Most Common Horticulture Customs Clearance Problems
Phytosanitary Certificate Errors
The phytosanitary certificate is issued by the plant protection authority in the exporting country, often the equivalent of the USDA APHIS. It certifies that the plants or plant products have been inspected and meet the importing country’s requirements.
Common phytosanitary certificate errors that cause shipment delays or rejections include:
- Scientific names that don’t match the commercial invoice
- Missing or incorrect treatment certifications
- Certificate issued too far in advance of shipment (some products require issuance within 14 days of export)
- Unsigned or improperly stamped documents (we’ve seen shipments held because an inspector’s stamp was too faint to read—seriously)
The USDA APHIS will not release cargo with a defective phytosanitary certificate and correcting it often requires coordination with the exporting country’s agriculture ministry. It’s rarely a same-day fix. (USDA APHIS Import Requirements)
Missing or Incorrect Import Permits
Certain plants, seeds, and soil require an import permit before they ship. The permit specifies approved ports of entry, packaging requirements, and inspection protocols.
No permit? The shipment gets refused or destroyed. Simple as that. Even shipments with a permit that don’t match the actual product (incorrect genus, incorrect treatment, incorrect port) face the same outcome. Import permits take weeks to get. Which means if you discover an error at the port, you’re out of luck.
Timing Misalignment and Inspection Backlogs
While fresh cut flowers, plants, and produce are time-sensitive, USDA inspections are not always immediate. Inspection priority can depend on:
- Commodity risk level (high-risk items like soil-bearing plants are inspected more thoroughly)
- Port capacity and staffing levels
- Seasonal volume surges (Valentine’s Day, Mother’s Day, and December holidays create inspection bottlenecks—and boy, do they create bottlenecks)
A horticulture freight forwarder who has established relationships at key ports can help manage timing, but the importer will still need to build extra time into delivery schedules. There’s just no getting around it.
State-Level Restrictions That Aren’t on Your Radar
Even after the shipment receives federal clearance, some states impose additional restrictions. California, Florida, Texas, and Hawaii all maintain aggressive pest and disease control programs. They will stop shipments at state borders if documentation doesn’t align with their requirements.
Example:
A shipment cleared by the CBP and the USDA in Miami for distribution to California may still require a California state agriculture inspection and compliance certification before entering the state. If the importer isn’t prepared for this, the shipment sits and waits.
FDA Prior Notice Errors for Edible Products
Edible products? Then you’re dealing with the FDA too. Prior Notice must be filed with the FDA before the shipment arrives, and it must accurately describe the product, manufacturer, and intended use.
Mismatches between Prior Notice and the actual cargo lead to FDA holds, which add days to clearance time. Two days can be the difference between sold and composted. (FDA Prior Notice Requirements)
What Delays Actually Cost
Horticulture importers work on tight margins. When a shipment is delayed in customs, costs add up fast:
- Demurrage charges and storage fees at the port or cold storage facility
- Product degradation or total loss when perishability limits are exceeded
- Customer penalties or rejections when delivery commitments are missed (and good luck getting that buyer back for the next order)
- Emergency expedited freight to recover a delayed shipment
- Reputational damage with buyers who depend on consistent supply
A single clearance issue can wipe out the profit on an entire container. Sometimes more than one.
How to Reduce Horticulture Customs Clearance Risk
Importers who move fresh products successfully treat compliance as something to handle before the shipment moves, not a last-minute scramble.
Here are some best practices to consider prior to shipping:
- Verify the phytosanitary certificate for accuracy before the product ships. Check (and then double check) scientific names, treatments, and certificate dates against your commercial documents.
- Confirm import permit requirements early. Some commodities require permits, which can take 30 or more days to obtain. It’s best to not assume your product is exempt.
- Use a customs broker with USDA APHIS expertise. Generic brokerage knowledge isn’t enough for horticulture. The broker needs to understand plant health regulations, state-level nuances, and agency communication protocols. Not just CBP basics.
- Plan for inspection time. Even clean shipments can take 24-48 hours to clear if inspections are required. Build that buffer into your supply chain schedule.
- Monitor seasonal volume surges. Importing flowers in early February? Expect delays.
How Zarach Logistics Handles Horticulture Clearance
At Zarach Logistics, an expert horticulture freight forwarder, we’ve cleared thousands of horticulture shipments over four decades, and we know the clearance window for fresh products doesn’t leave room for mistakes. Our team works directly with the USDA APHIS, the FDA, and state agriculture departments to manage pre-clearance document review, coordinate inspection timing, and resolve holds before they turn into losses.
We operate in key agricultural import hubs - New York, Chicago, Houston, and more - where horticulture volume is high and agency relationships matter. When a shipment needs expedited attention, we know who to call and how to get it moving.
Our horticulture customs clearance includes:
- Pre-arrival document review and compliance verification
- Direct coordination with USDA inspectors for timing and priority handling
- State-level permit and certification management
- FDA Prior Notice filing and FSMA compliance support
- Real-time status updates through our EZ Trace visibility platform
(CBP Agriculture Imports Overview)
Customs clearance for horticulture products isn’t general freight forwarding. The stakes are higher, the timeline is shorter, and the regulations are stricter.
When you’re moving perishable products, you need a partner who understands the complexity and manages it before it turns into a crisis. Call us. We’ll walk through your supply chain, identify the compliance gaps, and build a clearance strategy that protects your product and your margins.