A hash of hashes will do that nicely,

my %hoh;
my @labels = qw/SAN_Info Criticality_rating Commission_Date/;
while (<>) {
    my ($key, @dat) = split ',';
    $hoh{$key}{$labels[$_] ||= $dat[$_] for 0..$#labels;
}
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The ||= assignment prevents a filled slot from being overwritten by undef.