New Delhi, India – The vapour heat treatment (VHT) facility in Rehmanpur village of Lucknow, the capital of the northern Indian state of Uttar Pradesh – used to sterilise fruit and vegetables – was preparing for the busiest time of the year when Japanese quarantine inspectors turned up in March.

Export documents had been cleared, shipping schedules finalised, and growers in the western states of Maharashtra and Gujarat reserved their best Alphonso and Kesar mangoes for export to Japan, one of Asia’s premium markets.

Everything appeared set for the season to begin when production ground to a halt. Japanese inspectors reviewing the fumigation, disinfection and certification procedures raised concerns about the whole process, prompting Japan to suspend imports of the fruits.

However, on March 31, the plant protection authorities in Yokohama sent a formal letter, saying all Indian mango shipments bearing inspection certificates issued on or after March 25 would be barred until inspectors could confirm that operational standards had improved.

It was the first major disruption in India-Japan mango trade in nearly two decades. In 1986, imports of the fruit were barred over fruit fly concerns. Restrictions were lifted in 2006 after the country built VHT infrastructure, strengthened pest surveillance and agreed to annual inspections.

Japan ‘gave us credibility’

The 2026 halt now affects six approved varieties of mango – Alphonso, Kesar, Langra, Banganapalli, Chausa and Mallika – covering the peak export window of April through to June.

Japan imported roughly $1.54m worth of fresh and processed mango products from India between 2025 and 2026. It might appear to be a modest sum, but the Japanese market holds huge significance for the rest of the global trade. Japan pays premium prices for mangoes and the country’s approval signals quality to the rest of the world.

The suspension came at an already challenging time for mango farmers in India. Sustained heatwaves through the Konkan belt had destroyed much of Maharashtra’s Alphonso crop. Geopolitical disruptions in West Asia had pushed freight costs higher, and exporters who had spent years establishing relations with the Japanese suddenly faced cancelled contracts and inventories rotting in storage.

Vikram Shah, a Mumbai-based exporter who shipped about 2.5 tonnes of mangoes to Japan in 2025, highlighted the importance of its market.

“Japan was never our biggest market in terms of quantity, but it was the one that gave us credibility,” Shah told Al Jazeera. “We spent six years building trust with buyers there. I travelled to Osaka twice, sat with importers, visited their cold storage facilities and learned exactly what they expected from us. Relationships like that take years to build and can disappear in a single season.”

Rajesh Patil, an Alphonso grower in Ratnagiri, Maharashtra, said his family had cultivated mangoes on a three-acre (1.2-hectare) orchard along the Konkan coast for two generations. The Japanese market, he said, consistently delivered far higher returns than domestic auctions, leading him to invest heavily in meeting Japan’s stringent import standards.

“We upgraded the orchard because Japan rewarded quality,” Patil said. “I spent nearly ₹80,000 [$840] on grading and handling equipment, attended pest-management training sessions, and changed the way we harvest and pack fruit,” he told Al Jazeera.

“The Japanese market paid almost twice what I could earn locally. When you make those investments, you expect the system supporting exports to be as reliable as the fruit you grow.”

China objects to rice

On April 17, China revoked the import licences of three Indian rice exporters after the General Administration of Customs rejected their consignments, claiming traces of genetically modified organisms (GMO).

The exporters disputed the finding, pointing out that their shipments received GMO-free certification before their departure and that the Indian government also said all domestic paddy and rice fields are free of genetic modification.

Rice makes up more than 20 percent of India’s agricultural exports, with a record-breaking $12.5bn of it shipped in the last financial year (2025-26). The three suspended exporters now face an uncertain path back into China, rattling their community.

Agricultural and Processed Food Products Export Development Authority (APEDA), under India’s Ministry of Commerce and Industry, notified the companies and, on June 8, published a list of laboratories approved for GMO tests on China-bound shipments.

SK Singh, an agricultural scientist in New Delhi, told Al Jazeera the dispute exposed weaknesses in India’s testing system.

“Our labs built expertise in pesticide residue and aflatoxin testing because that’s what most markets wanted,” he said. “China’s demand for GMO verification calls for a different scale of capacity.”

The exporters’ certificates came from accredited labs even if the certification network remains uneven, he added.

Only a handful of facilities, concentrated in New Delhi and Hyderabad in the southeastern state of Telangana, run the required protein analysis, forcing exporters in northern Punjab and Haryana states to ship samples hundreds of kilometres away.

Fragmented supply chain

There were other warning signs before the crisis hit mangoes and rice.

Hong Kong suspended several Indian spice products over pesticide residues, and testing found quality deviations in nearly 12 percent of the samples. The European Union also raised the inspection frequency on Indian cumin to 30 percent in January 2025, following 312 spice alerts on its rapid alert system in 2024.

Ananya Bose, a food safety scientist in Kochi in the southern state of Kerala, traced the problem to a fragmented supply chain.

“A farmer sells to an aggregator, who sells to a trader, who supplies a processor. Somewhere in that chain, the record of what was sprayed disappears,” she said. “The trail is detailed until the first sale, then it effectively ends.”

Bose has pushed for mandatory digital pesticide records, since regulators abroad expect traceability from field to shipment, a standard many states still treat as optional.

These setbacks may read as isolated incidents, but they expose a gap between India’s agricultural strength and the traceability, food safety and certification standards that Japan, the EU, the United Kingdom, the United States and Canada now demand. Those standards are tightened by consumer pressure for transparency, climate-driven pest concerns, food-security strategy and the COVID pandemic.

At the same time, competitors have moved faster, with Thailand building a nationwide traceability programme, Vietnam investing in farmers’ training, and Brazil and Chile pouring money into cold-chain systems.

India’s progress has lagged with just 207 registered pack houses, 72 percent of them concentrated in Maharashtra. Moreover, scarce cold storage facilities and logistical costs eat up roughly 15 percent of export value, almost double that of advanced nations. Small farmers owning less than 2 hectares (5 acres) of land make up more than 86 percent of India’s cultivators, making standardisation difficult at scale.

“India built its strategy around producing more, while premium markets reward proving quality along the way,” agricultural economist Anil Gupta told Al Jazeera.

Gupta pointed to some real gains: recognised laboratories grew from 22 to 89 over the past decade, and approved export certificates climbed from roughly 61,000 to more than 170,000.

“The progress is measurable, but so is the scale of the challenge,” he said. “These improvements mark a beginning, well short of the finish line.”

Ujjwal Kumar Ghosh, a senior official in the government’s Department of Commerce, has called for tighter controls on antibiotic residues, pesticides and aflatoxins in spices, tea, fruits and vegetables. He said funds have been set aside to upgrade laboratories, though without a timeline.

“The government is strengthening the system from testing to inspection and traceability. We are tightening controls on antibiotic and pesticide residues and aflatoxins, expanding laboratory capacity, introducing risk-based inspections and using digital systems and rapid screening to identify problems faster. The objective is to help exporters meet stricter global food-safety standards while protecting India’s access to international markets,” said Ghosh.

India still holds just 2.4 percent of global agri-exports despite ranking as the world’s second-largest agricultural producer, with processed exports stuck near 17 percent, against 25 percent in the US and 50 percent in China.

And growers are facing the fallout.

Gujarat’s Kesar mango farmers lost their strongest Japanese buyer. A basmati rice farmer in Haryana’s Karnal said local prices had already dropped 8 percent. And a turmeric processor in Kerala’s Erode said residue testing cost him 15,000 rupees ($157) last quarter, almost 10 percent of his profit.

Agriculture still employs about 42 percent of India’s workforce while producing less than a fifth of the national output.

“This is about far more than a few rejected shipments,” Gupta said. “The countries that succeed will consistently meet the standards global buyers demand.”

Indian farmers have long proven they can grow for the world. The task now is building systems that convince the world to keep buying.