"Her prostitution studies have been criticized by sociologist Ronald Weitzer, for alleged problems with their methodology. In particular, Weitzer was critical of what he viewed as the lack of transparency in how the interviews were conducted and how the responses were translated into statistical data, as well as the sampling bias toward highly marginalized groups of sex workers (such as street workers) and for the way the findings of Farley's studies have been more generally applied to demonstrate the harm of sex work of all kinds. A 2002 study by Chudakov, et al. used Farley's PTSD instrument to measure the rate of post-traumatic stress disorder among sex workers in Israel. Of the fifty five consenting women interviewed, 17% met the criteria for PTSD, compared to Farley's 68% figure. Farley's critics also claim that her findings are heavily influenced by her radical feminist ideology.

Farley has also been criticized for accepting significant funding from anti-prostitution organizations. She has acknowledged that 30% of funding for a prominent research project into prostitution was provided by the United States Department of State Office to Monitor and Combat Trafficking in Persons, an agency with an outspoken policy which conflates sex work with human trafficking. However, Farley has stated that such funding has not in any way swayed her research, in particular its methods or conclusions."