The small-scale electron density irregularities in the ionosphere have a significant impact on the interruptions of Global Navigation Satellite System (GNSS) navigation and the accuracy of GNSS positioning techniques. The sporadic ionospheric E (Es) layer significantly contributes to the transient interruptions of signals (loss of lock) for GNSS tracking loops. These effects on the GNSS radio occultation (RO) signals can be used to derive the global location and intensity of Es layers as a complement to ground-based observations. Here we conduct statistical analyses of the intensity of Es layers, based on the scintillation index S4max from the FORMOSAT-3/COSMIC during the period 2006–2014. In comparison with simultaneous observations from an ionosonde network of five low-to-middle latitude ionosondes, the S4max indices from COSMIC, especially the small values, are linearly related to the critical frequency of Es layers (foEs). An accumulated period of less than 1 h is required to derive the short-term variations in real-time ionospheric Es layers. A total of 30.22%, 69.57% and 98.13% coincident hourly foEs values have a relative difference less than 10%, 30% and 100%. Overall, the GNSS RO measurements have the potential to provide accurate hourly observations of Es layers. Observations with S4max < 0.4 (foEs < 3.6 MHz), accounting for 66% of COSMIC S4 measurements, have not been used fully previously, as they are not easily visible in ground-based ionosonde data.