If it takes 3 seconds for FONCTION1() to run, and 4 seconds for FONCTION2(), your script waits 5 seconds for the next run. An alternative way would be:

my $next = time;
while (1) {
    $next  = time if $next < time;
    $next += 6;
    FONCTION1;
    FONCTION2;
    sleep $next - time;
}
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This still has all the caveats of using sleep (may sleep longer, may be terminated by a signal, may actually sleep for a second if the argument is 0), but it won't miss its "slot" if a run of FONCTION1(); FONCTION2() takes more than 6 seconds.