Why Indian agricultural exports are facing rising scrutiny abroad

New Delhi, India – The vapor heat treatment (VHT) facility in Rehmanpur village, on the outskirts of Lucknow, capital of Uttar Pradesh state, was gearing up for its busiest time of year when Japanese quarantine inspectors arrived unexpectedly in March.

Export paperwork had been cleared, shipping schedules were locked in, and mango farmers in the western states of Maharashtra and Gujarat had set aside their best Alphonso and Kesar fruits for Japan, one of Asia's premium markets.

Everything seemed ready for the new season when production suddenly ground to a halt. The Japanese inspectors, reviewing the fumigation, disinfection, and certification process, raised concerns, leading Japan to suspend imports of Indian mangoes.

On March 31, the plant protection agency in Yokohama sent a formal notice stating that all Indian mango shipments carrying quarantine certificates issued on or after March 25 would be denied entry until inspectors confirmed that operational standards had been improved. This marks the first major disruption in India-Japan mango trade in nearly two decades. In 1986, Indian mangoes were banned over fruit fly concerns. The ban was only lifted in 2006 after India built VHT infrastructure, stepped up pest surveillance, and agreed to annual Japanese inspections.

The 2026 import halt affects six mango varieties approved for export – Alphonso, Kesar, Langra, Banganapalli, Chausa, and Mallika – during the peak export season from April to June.

Japan imported about $1.54 million worth of fresh and processed mangoes from India during the 2025-2026 period. The figure may seem modest, but the Japanese market carries significant weight in global trade. Japan pays premium prices for mangoes, and its approval is seen as a quality signal for the rest of the world.

The suspension comes at a difficult time for Indian mango farmers. Prolonged heat across the Konkan region has devastated much of Maharashtra's Alphonso crop. Geopolitical instability in West Asia has driven up shipping costs, and exporters who spent years building relationships with Japanese partners suddenly face canceled contracts and perishable stock rotting in cold storage.

Vikram Shah, an exporter in Mumbai, shipped about 2.5 tons of mangoes to Japan in 2025. He stressed the importance of this market. "Japan was never our largest market, but it's the one that brings prestige. We spent six years building trust with buyers there. I've been to Osaka twice, sat down with importers, toured their cold storage facilities, and learned exactly what they expect. Relationships like that take years to build and can disappear in a single season."

Rajesh Patil, an Alphonso mango farmer in Ratnagiri, Maharashtra, said his family has worked a 1.2-hectare orchard along the Konkan coast for two generations. The Japanese market has always paid significantly more than domestic auctions, so he invested heavily to meet Japan's stringent import standards. He spent nearly $1,840 on sorting and handling equipment, attended training sessions on pest management, and changed his harvesting and packaging methods. "The Japanese market pays nearly double what we get at home. When you invest like that, you expect the export support system to be as reliable as the fruit you grow."

China pushes back on rice

On April 17, China revoked the import licenses of three Indian rice exporters, after the country's General Administration of Customs rejected shipments citing traces of genetically modified organisms (GMO). Exporters rejected the finding, pointing out that their shipments had non-GMO certification before leaving port, and the Indian government has also affirmed that no genetically modified rice is grown in the country.

Rice accounts for more than 20% of India's agricultural export value, hitting a record $12.5 billion in the last fiscal year (2025-2026). The three suspended exporters now face a difficult path back into the Chinese market, sending shockwaves through the industry.

The Agricultural and Processed Food Products Export Development Authority (APEDA), under India's Ministry of Commerce and Industry, has notified the companies and on June 8 published a list of approved laboratories for GMO testing of shipments to China.

SK Singh, an agricultural scientist in New Delhi, said the case exposed weaknesses in India's testing system. "Our labs are good at testing for pesticide residues and aflatoxin because that's the standard most markets require. China's demand for GMO verification requires a whole different scale of capability." Exporters' certificates come from accredited labs, but the certification network remains uneven. Only a few facilities, mainly in New Delhi and Hyderabad, can run the protein analysis tests required, forcing exporters in Punjab and Haryana to send samples hundreds of kilometers.

Fragmented supply chain

There were warning signs before the mango and rice crises. Hong Kong suspended several Indian spice products over pesticide residues, with quality discrepancies detected in nearly 12% of samples. The European Union also increased inspection frequency for Indian cumin to 30% starting January 2025, following 312 alerts about spices on the bloc's rapid alert system in 2024.

Ananya Bose, a food safety scientist in Kochi, Kerala, pointed to the fragmented supply chain as the root problem. "Farmers sell to aggregators, aggregators sell to traders, traders supply processors. Somewhere along that chain, records of pesticide application disappear. Traceability is detailed up to the first sale, then it almost ends."

Bose suggested making electronic records of pesticide use mandatory, as foreign regulators require traceability from field to shipment, a standard that many states still treat as voluntary.

These setbacks could be seen as isolated incidents, but they expose the gap between India's agricultural strength and the traceability, food safety, and certification standards demanded by Japan, the EU, the UK, the US, and Canada. Those standards are being tightened by consumer pressure for transparency, pest concerns linked to climate change, food security strategies, and the COVID-19 pandemic.

Meanwhile, competitors have moved faster, with Thailand building a national traceability program, Vietnam investing in farmer training, and Brazil and Chile pouring money into cold chain systems.

India's progress has been slow, with only 207 registered packing houses, 72% of them concentrated in Maharashtra. Cold storage facilities are scarce, and logistics costs account for about 15% of export value, nearly double that of developed countries. Farmers with less than 2 hectares make up more than 86% of cultivators, making large-scale standardization difficult.

Anil Gupta, an agricultural economist, observed: "India's strategy has focused on producing more, while premium markets reward demonstrating quality throughout the process." He acknowledged tangible improvements: the number of accredited labs has grown from 22 to 89 over the past decade, and the number of approved export certificates has risen from about 61,000 to over 170,000. "Progress is measurable, but the scale of the challenge is also huge. These improvements are just the beginning, far from the finish line."

Ujjwal Kumar Ghosh, a senior official at the Ministry of Commerce, called for tighter controls on antibiotic, pesticide, and aflatoxin residues in spices, tea, fruits, and vegetables. He said a budget has been allocated to upgrade laboratories, but did not provide a specific timeline.

India currently accounts for only 2.4% of global agricultural exports despite being the world's second-largest agricultural producer. Processed agricultural goods make up only about 17% of its exports, compared to 25% in the US and 50% in China.

Farmers are bearing the brunt. Kesar mango growers in Gujarat have lost their biggest Japanese buyer. A basmati rice farmer in Karnal, Haryana, said local paddy prices have dropped 8%. A turmeric processor in Erode, Kerala, said residue testing costs consumed nearly $157 last quarter, close to 10% of his profit.

Agriculture still employs about 42% of India's workforce but contributes less than one-fifth of the country's GDP.

"This isn't just about a few shipments being sent back. The countries that succeed will be those that consistently meet the standards global buyers demand," Gupta said. Indian farmers have long proven they can grow for the world. The task now is building the system to convince the world to keep buying.