The central shaft is an inseparable part of a vertical axis wind turbine (VAWT). For small turbines such as those typically used in urban environments, the shaft could operate in the subcritical regime, resulting in large drag and considerable aerodynamic power loss. The current study aims to (i) quantify the turbine power loss due to the presence of the shaft for different shaft-to-turbine diameter ratios δ from 0 to 16%, (ii) investigate the impact of different operational and geometrical parameters on the quantified power loss and (iii) evaluate the impact of the addition of surface roughness on turbine performance improvement. Unsteady Reynolds-averaged Navier-Stokes (URANS) calculations are performed on a high-resolution computational grid. The evaluation is based on validation with wind-tunnel measurements. The results show that the power loss increases asymptotically with increasing δ due to the higher width and length of the shaft wake as the blades pass through a larger region with lower velocity in the downwind area. A maximum power loss of 5.5% compared to the hypothetical case without shaft is observed for δ = 16%. The addition of surface roughness is shown to be an effective approach to shift the flow over the shaft into the critical regime, reducing the shaft drag and wake width as a result of a delay in separation. For an optimal dimensionless equivalent sand-grain roughness height of 0.08, the turbine power coefficient at δ = 4% improves by 1.7%, which is equivalent to a 69% recovery of the corresponding turbine power loss. The results are found to be virtually independent of the shaft-to-turbine rotational speed ratio.