Successive waves of COVID-19 transmission have led to exponential increases in new infections globally. In this study, we have applied a decision-making tool to assess the risk of continuing transmission to inform decisions on tailored public health and social measures (PHSM) using data on cases and deaths reported by Member States to the WHO Regional Office for Africa as of 31 December 2020. Transmission classification and health system capacity were used to assess the risk level of each country to guide implementation and adjustments to PHSM. Two countries out of 46 assessed met the criteria for sporadic transmission, one for clusters of cases, and 43 (93.5%) for community transmission (CT) including three with uncontrolled disease incidence (Eswatini, Namibia and South Africa). Health system response's capacities were assessed as adequate in two countries (4.3%), moderate in 13 countries (28.3%) and limited in 31 countries (64.4%). The risk level, calculated as a combination of transmission classification and health system response's capacities, was assessed at level 0 in one country (2.1%), level 1 in two countries (4.3%), level 2 in 11 countries (23.9%) and level 3 in 32 (69.6%) countries. The scale of severity ranged from 0 to 4, with 0 the lowest. CT coupled with limited response capacity resulted in a level 3 risk assessment in most countries. Countries at level 3 should be considered as priority focus for additional assistance, in order to prevent the risk rising to level 4, which may necessitate enforcing hard and costly lockdown measures. The large number of countries at level 3 indicates the need for an effective risk management system to be used as a basis for adjusting PHSM at national and sub-national levels.