The drug regulator is in the midst of a review of over 300 jobs in its organisation to determine whether they could be more cost-competitively carried out by external contractors.
Positions under threat are those that are determined by the agency as commercial and therefore, under current law, can be carried out by non-government employees.
The original list included laboratory and field staff affiliated with food and drug safety testing facilities although after an outcry the list was recently revised to include only administrative jobs that are not directly involved in safety matters.
Outsourcing is now commonplace throughout the pharmaceutical industry with very few functions left that are not exposed to potential externalisation.
Safety and regulatory roles, however, remain sacred, and considering these are the FDA's primary functions, there has been much concern expressed over the agency's plans to place any roles affiliated with such responsibility in external hands.
An agency spokesperson stressed that none of the jobs being considered for outsourcing are directly involved in the inspection and enforcement.
It also insisted that it is "obligated" to undertake this job scrutiny as part of "competitive sourcing initiatives set forth by the Office of Management and Budget and the Department of Health and Human Services in response to the President's management agenda".
According to the spokesperson, the agency has managed to save over $13m (€9.6m) through such initiatives since 2003.
The drug regulator is due to complete its assessments by the end of September, after which point a decision will be made as to who will go and who will stay.
However, the National Treasury Employees Union (NTEU), which represents over half of the FDA's 9,000 employees, said it intends to lobby Congress to block any job losses at the agency.
The NTEU has already recently had a partial victory in pursuading Congress to intervene in the FDA's plans to close a number of safety testing labs across the country, which have now, as a result, been shelved.
The drug regulator had been planning to reorganise its Office of Regulatory Affairs (ORA), which would have consolidated 13 laboratories into five and seen the closure of the remainder.
The NTEU recently expressed delight at the FDA's announcement that it would abandon its planned ORA reorganisation, although the FDA has since clarified the situation, by saying that its plans are at this point not cancelled, but only "temporarily suspended", pending the outcome of re-evaluation and consultation, including recommendations from a newly-formed Interagency Working Group on Import.