#!/usr/bin/perl -w
use strict;
use Data::Dumper;
use Sort::Key::Multi qw(iikeysort);

chomp( my @s = <DATA> );
my @is = iikeysort {
    /\A .+ _ (\d+) _ (\d+) .+ txt \z/msx;
}
@s;
print Dumper \@is;

__DATA__
M3_output_ZGZ22_02_20061022_duration_200mn_comptage_60.txt
M3_output_ZGZ22_078902_20061022_duration_200mn_comptage_60.txt
M3_output_ZGZ22_11_20061022_duration_200mn_comptage_60.txt
M3_output_ZGZ22_1_20061022_duration_200mn_comptage_60.txt
M3_output_ZGZ22_078902_20051022_duration_200mn_comptage_60.txt
M3_output_ZGZ22_128_20061022_duration_200mn_comptage_60.txt
[download]

Output:
$VAR1 = [
          'M3_output_ZGZ22_1_20061022_duration_200mn_comptage_60.txt',
          'M3_output_ZGZ22_02_20061022_duration_200mn_comptage_60.txt'
+,
          'M3_output_ZGZ22_11_20061022_duration_200mn_comptage_60.txt'
+,
          'M3_output_ZGZ22_128_20061022_duration_200mn_comptage_60.txt
+',
          'M3_output_ZGZ22_078902_20051022_duration_200mn_comptage_60.
+txt',
          'M3_output_ZGZ22_078902_20061022_duration_200mn_comptage_60.
+txt'
        ];
[download]

hth,
PooLpi