Agricultural practices are often responsible for environmental degradation, such as non-sustainable food production, poor fuel use, natural resource depletion and habitat exploitation.
The warnings come in the form of a report prepared in advance of the FAO Committee on Agriculture meeting, which gets underway in Rome today.
Alexander Müller, FAO Assistant Director-General said that farmers are key players in stopping degradation of vital ecosystems but it is a fundamentally political matter, which requires changes in agricultural policies, institutions and practices.
"Much of the discussion regarding biodiversity, climate change and bioenergy is currently taking place without the effective participation of the agricultural sector and ministries," Müller said.
"This needs to be changed.
Furthermore, we urgently need a global analysis about the environmental risks associated with agriculture, a strategic framework for identifying ecologically and economically sound approaches."
The concern over agricultural practices is set against a back-drop of climate change, which is also having an impact on food production - despite environmental agreements aimed at curbing the impact.
In particular, the FAO report draws attention to still-rising carbon emissions, extinction of species, and desertification.
As temperatures rise, production systems are expected to become destabilized by water shortages, salinity, aridity.
What is more, anticipated growth in biofuel monoculture is expected to speed up biodiversity erosion - a detracting factor to biofuels' halo as a sustainable alternative to fossil fuels.
"These changes pose great challenges because biodiversity is the raw material that breeders use to create the new crop varieties that will be needed to safeguard biodiversity for food and agriculture for future generations as well as maintaining a broad gene pool," the report said.
Unless addressed, all of these factors add up to a grim future for world food security, especially since world population growth shows no sign of slowing down - meaning that agricultural production and food availability must cater to more mouths.
The FAO has previously stressed that good agricultural practices could help developing countries cope with globalisation while not compromising their sustainable development objectives.
At an FAO seminar in January Paola Termine from the Sustainable Agricultural and Rural Development Programme said that such practices could contribute to a better environmental and social development at both national and international levels.
"For example, improvements in agricultural practices, such as integrated production and pest management, can lead to substantial improvements not only in terms of yield and production efficiencies but also in health and safety of workers," said Termine.
The week's meeting in Rome will also cover reduction of environmental damage cause by livestock production - an important factor since global meat and milk production is expected to double by 2050, from 1999/2001 levels of 465m and
580m tonnes respectively.
Most of this projected production growth will come from developing countries, and intensive systems will be the main contributor.
"Major political and technical corrections need to be taken to address the environmental impact of livestock production that will otherwise worsen dramatically, given the projected expansion of the livestock sector," Müller said.
The FAO is drawing attention to the stress that livestock production exerts on many ecosystems - such as degradation of grassland, carbon dioxide and methane emissions, and global water use.