Functional Capacity Evaluations (FCE's) are not a regulated or controlled act. You can perform an FCE if it is in your scope of practice.
That said, like with most unregulated things, there is some self regulation. You should check your local referral sources, they may have restrictions.
As an example in the state of California, according to The Physical Therapy Board of California, a Physical Therapy Assistant (PTA) cannot perform a "physical therapy FCE". However a PTA can perform a "pre-employment FCE".
Do I need to be certified?
Since the FCE is not regulated there is no requirement to be certified. However certification can help in the following ways:
a) Getting approval or payment: You may be asked to provide proof you are qualified to perform an FCE. "Current Concepts in Functional Capacity Evaluation — A Best Practices Guideline" published by the Occupational Health Special Interest Group of the American Physical Therapy Association states that an FCE examiner should be "able to demonstrate evidence of education, training, and competencies specific to the design, administration, and interpretation of FCEs"
b) Providing expert testimony: The Daubert Standard is used by a trial judge to assess whether an expert witness’s scientific testimony is based on scientifically valid reasoning that which can properly be applied to the facts at issue. You may be asked to provide proof that you are an expert. A witness who is qualified as an expert by knowledge, skill, experience, training, or education may testify in the form of an opinion.
Read more about Metriks FCE certification.