This method it use .cue files, which usually comes with the .flac ones.
First of all we need to install the following packages cuetools shntool flac. You can use Synaptic or this command in a terminal:
$ sudo apt-get install cuetools shntool flac
Now you can split the .flac audio file as follows:
$ cuebreakpoints file.cue | shnsplit -o flac file.flac
Now a little bit of theory,
... shnsplit is the program used to split tracks, while cuebreakpoints it reads the break-points from file.cue and pipe them to shnsplit.