Macron was supposed to close the day's deliberations on the national diet but, following the resignation of chief of staff Pierre de Villiers over budget cuts, he prolonged a visit to the Istres air base, a key location for France's nuclear arsenal.
There he tried to calm the troops with an assurance that the defence budget will be the only one to rise in 2018, adding that he was sticking to his commitment to raise it to two percent of GDP by 2025.
Farmers worried about retail pressure on prices
There are frequent protests on the question, most recently in relation to apricots, peaches and milk, a long-running cause for concern.
"Why does part of the value [realised] not go back down from retail to production?" he asked.
But, he added, "I am not here to name the guilty parties but to find solutions. Not short-term solutions while we wait for the next crisis but lasting solutions in the context of normal business relations. The state cannot replace the market."
Food's shrinking share of French consumer spending
French households spend 20 percent of their incomes on food, compared to 35 percent in the 1960s, according to a report by statistics institute Insee in 2015.
The main explanation is the rise in spending power, up over 10 percent between 1960 and 1990.
A small rise, 0.33 percent, has been reported between 2012 and 2016.
Consumers are buying more organic produce, with a 21.7 percent rise in 2016 compared to 2015, according to the organic agency.
Meat represented 15 percent of food spending in 2014, compared to 20 percent in 1960, although the figure is partly due to the increase in take-away foods and eating in restaurants.
The meeting brings together various interested parties - farmers, consumers, agribusiness, retailers, environmental campaigners, health professionals, along with representatives of 11 ministries and the European Commission.
Macron was not the only person to cry off on Thursday - Health Minister Agnès Buzyn was represented by top health official Benoît Vallet and Economy Minister Bruno Le Maire ceded his place to junior minister Benjamin Griveaux in the afternoon.
The two politicians with most riding on the event - Environment Minister Nicolas Hulot and Agriculture Minister Stéphane Travert - were there, however.
The consultation was Hulot's brainchild, adopted by Macron during his presidential campaign before he persuaded the veteran green campaigner to join his government.
Conflicting interests of NGOs, farmers, consumer groups
There were reports of tension between the two ministers in the runup to the meeting - a reflection of the conflicting concerns of some farmers and environmentalists.
The largest farmers' unions are most worried about their members' incomes, doing battle with the supermarkets over prices and tending to favour large-scale production both for the domestic and export markets.
Many NGOs - along with health professionals and one left-wing farmers' union - favour a transition from industrialised agriculture to environmentally friendly models, such as organic farming and buy-local initiatives.
Meanwhile, the main consumer group, UFC Que Choisir, is worried about prices, which could pit it against both the farmers and the ecologists.
Costs of intensive farming
The problems caused by intensive farming have also become a matter of concern for governments, which have to deal with land and water pollution, exposure to pesticides, destruction of biodiversity and greenhouse gas emissions.
Cleaning up water pollution from agriculture, for example, costs France 54 billion euros a year, according to a 2011 study by the Environment Ministry.
But NGOs regret that subjects like adaptation to climate change, animal rights and the marine environment are not on the agenda and fear that commercial pressures will squeeze out their concerns.
During the election campaign, Macron promised five billion euros to modernise agriculture.
It should not "simply be used to renovate buildings, increase the size of herds and build dams to water maze", the WWF campaign said before the conference.
The deliberations, which will break up into workshops, will go on until mid-November.
An internet consultation has also been launched, although it is not yet clear how its findings will be included in the final conclusions.