You could try

1) Use the alarm function to raise a signal after a number of seconds

eval {
   local $SIG{ALRM}=sub { die "ALARM\n" };  # \n is required
   alarm 300;   # give it 5 minutes
   # your code here
   alarm 0;     # reset alarm
};
if ($@ eq "ALARM\n") {
   print "Timed out!\n";
}
[download]

2) Use Apache TimeOut directive

3) Use Time::Out, it looks cool and is well-documented.

Hope that helps,
SSF