A fundamental assumption in this interpretation of the f-ratio is the spatial separation of primary production and nitrification.  Indeed, in their original paper, Eppley & Peterson noted that: "To relate new production to export requires that nitrification in the euphotic zone be negligible."  However, subsequent observational work on the distribution of nitrification has found that nitrification can occur at shallower depths, and even within the photic zone.
As the adjacent diagram shows, if ammonium is indeed nitrified to nitrate in the ocean's surface waters it essentially "short circuits" the deep pathway of nitrate.  In practice, this would lead to an overestimation of new production and a higher f-ratio, since some of the ostensibly new production would actually be fuelled by recently nitrified nitrate that had never left the surface ocean.  After including nitrification measurements in its parameterisation, an ecosystem model of the oligotrophic subtropical gyre region (specifically the BATS site) found that, on an annual basis, around 40% of surface nitrate was recently nitrified (rising to almost 90% during summer).  A further study synthesising geographically diverse nitrification measurements found high variability but no relationship with depth, and applied this in a global-scale model to estimate that up to a half of surface nitrate is supplied by surface nitrification rather than upwelling.
Although measurements of the rate of nitrification are still relatively rare, they do suggest that the f-ratio is not as straightforward a proxy for the biological pump as was once thought.  For this reason, some workers have proposed distinguishing between the f-ratio and the ratio of particulate export to primary production, which they term the pe-ratio.  While quantitatively different from the f-ratio, the pe-ratio shows similar qualitative variation between high productivity/high biomass/high export regimes and low productivity/low biomass/low export regimes.
In addition, a further process that potentially complicates the use of the f-ratio to estimate "new" and "regenerated" production is dissimilatory nitrate reduction to ammonium (DNRA). In low oxygen environments, such as oxygen minimum zones and seafloor sediments, chemoorganoheterotrophic microbes use nitrate as an electron acceptor for respiration, reducing it to nitrite, then to ammonium. Since, like nitrification, DNRA alters the balance in the availability of nitrate and ammonium, it has the potential to introduce inaccuracy to the calculated f-ratio. However, as DNRA's occurrence is limited to anaerobic situations, its importance is less widespread than nitrification, although it can occur in association with primary producers.