If you want to do something that long and insert a silence in every 3 secs you’re going to not do it by hand, that’s for sure. You do need an automated process, thats for sure and I’m fairly certain thats what you were hinting at.
Unfortunately there is no way I know to do this in Audition. Logic however has a “Tremolo” plugin which you should be able to utilise to such an effect. Given this is Audition you can get yourself a cheap Tremolo VST plugin that allows you to achieve such an effect.

You need to be able to select a a time in seconds for it to cycle, you will need an asymmetrical looking square wave similar to the one in the main pane of the plugin in this pic. In Logic this was achieved by setting the Smoothing parameter to 0 and Symmetry up to around 80 or so.
The Depth and Mix (or Wet/Dry) if it has one you will want to set all the way up. Phase should be 0, and the Rate should either be 3 seconds or 0.33 Hz, which works out to be a 3 second period.
If you use the Tremolo in this manor it will drop audio every 3 secs for a short period. You then just need to render the VST and it will effect the entire duration of the audio.