It clearly has to do with log reduction, as you correctly pointed out. In order for a chemical disinfectant or antiseptic product to be characterized as such and prove its antimicrobial activity, an at least 5 decimal log reduction shall be demonstrated for this product. This is why you see "it kills 99.9999% of bacteria" written on the label of relevant products...

So, in terms of performance, the two antimicrobials tested with 99.99% and 99.9999% respective reduction values should have approximately a 2 log difference in antimicrobial activity.

Log and Percent Reductions in Microbiology and Antimicrobial Testing

http://microchemlab.com/log_reduction_and_percent_reduction_calculations

a clear relation is given

99.9 %= 1 log reduction

99.99%+ 2 log reduction

 As per Log and Percent Reductions in Microbiology and Antimicrobial Testing, following are the  log reductions :- 

 1 log reduction = 90% reduction

2 log reduction = 99 % reduction

3 log reduction = 99.9% reduction

4 log reduction = 99.99 % reduction

5 log  reduction = 99.999% reduction

6 log reduction = 99.9999% reduction 

99.9%=4 log reduction