This comment was posted on the federal FDA docket /rulemaking related to the “Guide to Minimize Microbial Food Safety Hazards for Fresh Fruits and Vegetables.” It was submitted by the Georgetown University linked O'Neill Institute regarding USDA AMS authority over food safety. It flatly challenges the authority of USDA to have any role in produce safety oversight.

Here is what the O’Neill Institute says on their Web site about who they are:

The O'Neill Institute draws on the expertise of nationally and internationally recognized experts on law and health. Affiliated faculty come from a variety of academic and research fields covering multiple disciplines. Below is a partial list of Institute faculty, staff, and fellows. This list is ever-growing, but provides an overview of the Institute's diverse capacity.  Recognizing the intellectual breadth of Georgetown University, the Institute is continually conducting outreach to faculty and institutions across campuses. In an effort to explore and build a diverse portfolio of health law projects, it is vital to create collaborative relationships with faculty who possess a diverse set of interests nd expertise.

Some excerpts from the comment:

TO: The Produce Safety Project
DATE: June 8, 2009

RE: USDA Authority regarding produce safety

This memorandum reviews the U.S. Department of Agriculture’s authority over produce safety. It provides an overview of the activities within the Agricultural Marketing Service (AMS) that may relate to the oversight of produce, in particular, produce safety.

In general, the U.S. Department of Agriculture (USDA) has no authority to enforce safety standards and take action to remove unsafe produce from the market; that authority rests with the U.S. Food and Drug Administration.
Numerous USDA agencies such as the Farm Service Agency (FSA), the Animal and Plant Health Inspection Service (APHIS),2 and the Agricultural Marketing Service (AMS), operate as service providers for the agricultural sector (e.g., responding to farmers’ financial, marketing, and trade issues, and protection of plant and animal health), rather than as bodies that enforce safety requirements.
Because of their association with agriculture, these agencies do administer programs that pertain to fresh produce. This memorandum will focus on AMS, which is the agency that works most directly with fresh produce. FDA, not AMS, has the legal authority to regulate produce safety.
In recent testimony before Congress, the Acting AMS Administrator reiterated this fact, stating that “FDA is the federal agency with primary responsibility for the food safety of fruits and vegetables. . . . AMS is not a food safety agency.” 

He went on to explain that AMS marketing orders and agreements do occasionally address safety-related issues because “[t]he presence or absence of harmful pathogens, toxins, or other contaminants is considered a quality characteristic.” Regarding the proposed National Marketing Agreement for Leafy Greens, the Acting Administrator emphasized that any under such an agreement “would be consistent with FDA guidance and eegulations requirements” and that “[a]ny product deemed an immediate threat to public health by USDA inspection would be reported by USDA to FDA.”

TK: The paper seems opposed to the USDA playing any role in produce safety. More from the report:

Currently, AMS oversees orders for 22 produce commodities.16 The question at issue is whether these agreements and orders serve to “regulate” food safety – i.e. whether AMS can take action to remove “adulterated” (unsafe) commodities from the market.

The language of the AMAA is clear that these programs are meant to be tools to “stabilize market conditions.” However, in at least two existing marketing orders, safety issues are addressed because they can impact negatively on market conditions. Additionally, there is a pending proceeding regarding leafy greens that may deal with safety concerns.

TK: Later, the paper said:

The distinction between food safety and food quality is more clearly explained in the joint U.N. FAO/WHO report, “Assuring Food Safety and Quality: Guidelines for Strengthening National Food Control.”  “Food safety refers to all those hazards, whether chronic or acute, that may make food injurious to the health of the consumer. It is not negotiable. Quality includes all other attributes that influence a product’s value to the consumer.
This includes negative attributes such as spoilage, contamination with filth, discoloration, off odours and positive attributes such as the origin, colour, flavour, texture and processing method of the food.

TK: The paper talks about the rulemaking on a potential national marketing agreement for leafy greens:
From the paper:

Comments to the ANPR are available online.34 Although some federal agencies submitted comments, interestingly, FDA apparently did not.35 Comments from federal and state agencies, and concerned consumers organizations did not address the issue of whether AMS was within its legislative authority to promulgate such a regulation.36 The pertinent question for many of the respondents was not whether AMS has the legal authority to regulate produce safety in this manner, but whether it should. Primarily, the issue was raised whether a marketing agreement is an appropriate mechanism for produce safety regulation.
The Consumers Union argued that marketing agreements (and orders) “were designed to establish and maintain orderly marketing conditions for regulated commodities, not to ensure the safety of those commodities.”37 The Center for Science in the Public Interest (CSPI) noted that AMS’s proposed marketing agreement may circumvent FDA’s authority to legitimately regulate produce safety. Additionally, the U.S. Environmental Protection Agency (EPA) and the U.S. Department of Commerce (through the National Marine Fisheries Services) wrote of their concerns about environmental degradation as a result of the order.
Both comments noted that in the aftermath of the California agreement, individual buyers and handlers (e.g., chain grocery stores and fast food chains) exceeded the requirements of the agreement. EPA commented “that many of these practices are not scientifically based, and have unintended consequences to the environment.”39

TK: Has this issue been settled or not? It seems there are some who would not like to see USDA play a role in oversight of food safety in marketing orders and promotion agreements, the wishes of the industry and the opinion of USDA lawyers notwithstanding. Perhaps the most important opinion – which so far cannot be pined down  – will be the from the FDA.