WTO Director-General Ngozi Okonjo-Iweala said the rules were now well out of date, with climate change and rapid population growth contributing to food security concerns.
"Too often, markets for food and agriculture still continue to function poorly," she said.
"It's increasingly clear that WTO rules have not kept pace with the challenges we face today, nor with developments on global markets."
A WTO statement said Monday's session heard that food systems were under increased strain from climate-induced water insecurity and drought, environmental degradation, Russia's war in Ukraine, and the lingering effects of the Covid-19 pandemic
Okonjo-Iweala said trade distortions and high levels of protection were a serious problem, while persistent under-investment in research and infrastructure had led to low and stagnating agricultural productivity in many regions.
Food export restrictions also continue to exacerbate the effect of price spikes on poor consumers in food-importing countries.
Nigeria-born Okonjo-Iweala called a one-day gathering at the global trade body's headquarters in Geneva on Monday aimed at finding ways through the logjam.
WTO member states have been negotiating on agriculture trade since 2000.
The group's last ministerial conference in June concluded with deals on curbing harmful fishing subsidies, bolstering food insecurity and temporarily waiving patents on Covid-19 vaccines.
Reaching these agreements -- where consensus is needed among all members -- revived the organisation, which had failed to strike any significant deals for nearly a decade.
The 13th WTO Ministerial Conference is due to take place before the end of 2023. Cameroon and the United Arab Emirates have offered to host the meeting.