You need to have a scout in your fleet as they're the only objects that I think can view mines.
What I do is put the scounts ahead of my fleet and then let my collective group knock down the mines when the scout reveals mines. It does takes sometime, but i gets the job done. I hope they're thinking about putting a mine sweeping fuction in for one of the vessels to speed up the process. As it does take some time to do it this way.
