If they're not bundled in the same distribution (.tar.gz) file then you could put prerequisites in the Makefile.PL of each separate module. Since you said you use ExtUtils::MakeMaker, I've done that with:
#
# $Id: Makefile.PL 49 2009-05-31 13:15:34Z $
#
use ExtUtils::MakeMaker;
require v5.6.1;
WriteMakefile(
NAME => 'Module::Name',
VERSION_FROM => 'lib/Module/Name.pm',
LICENSE => 'artistic',
ABSTRACT_FROM => 'lib/Module/Name.pm',
AUTHOR => 'VinsWorldcom',
PREREQ_PM => {
Business::ISP::m1 => 1.00 # must be greater than ver 1
Business::ISP::m2 => 0 # version doesn't matter
},
);