Partial degradation of high ammonia natural rubber (HANR) in the latex stage was successfully carried out in the presence of periodic acid as a water-soluble degrading agent at ambient temperatures, i.e. 30 °C. The number average molecular weight (Mn), weight average of molecular weight (Mw), gel content and Mooney viscosity were decreased as the periodic acid concentrations increased. The polydispersity was slightly increased with increasing periodic acid concentrations. The relationship between Mw, gel content and Mooney viscosity was established. Mw in the range of 8.0 × 105 g/mol to 1.2 × 106 g/mol, and gel content between 30 and 45 wt% successfully achieved the Mooney viscosity of raw natural rubber ranging from 60 to 85 MU. To obtain such properties, periodic acid concentration between 17 and 19 phr was used to partially degrade the natural rubber in the latex stage. The structural characterisations determined by Fourier transform infra-red (FTIR) and nuclear magnetic resonance (NMR) spectroscopies confirmed the occurrence of chain scission to form carbonyl terminal groups as a result of partial degradation. In summary, the Mooney viscosity of raw natural rubber can be controlled by partial degradation of natural rubber in the latex stage, contributed by a controlled decrease in molecular weight and gel content. Hence, this work may be useful in altering the properties of raw natural rubber that are suitable for processing of dry rubber products.