#!/usr/bin/perl

use strict;
use warnings;
use Proc::Reliable;

my $proc = Proc::Reliable->new( 'num_tries'    => 5,
                                'time_per_try' => 60,
                                'maxtime'      => 60);
Proc::Reliable::debug(1);

my $out = $proc->run('java -jar program.jar');
if($proc->status) {
    print($proc->stderr);
    exit;
}
else {
    print($proc->stdout);
}
[download]

Here is an example from alarm in the perlfunc manpage:

eval {
    local $SIG{ALRM} = sub { die "alarm\n" }; # NB: \n required
    alarm $timeout;
    $nread = sysread SOCKET, $buffer, $size;
    alarm 0;
};
if ($@) {
    die unless $@ eq "alarm\n";   # propagate unexpected errors
    # timed out
}
else {
    # didn't
}
__END__
[download]

You could probably adapt this to do what you need.

Update: Link fixed.

I wrote a couple of scripts a couple of years ago, one for Unix, one for Windows:

• Timing and timing out Unix commands
• Timing Windows commands

For Unix, this suggestion by ikegami looks good. What platform are you running on? For Windows, I suggest Win32::Job.