tye's mapcar solution is pretty elegant. Here's what I came up with to preprocess the list of rows before sending to Text::Table:

my @lines = (
  [ 1, '...', '...', '...', '...' ],
  [ 2, '...', "NA\nEU\nThird line", "Emp\nEx-emp", "Active\nInactive" 
+],
  [ 3, '...', '...', '...', '...' ]
);

for (my $l = 0; $l < @lines; $l++) {
    next unless grep /\n/, @{ $lines[$l] };
    splice @lines, $l+1, 0, [];

    ($lines[$l][$_], $lines[$l+1][$_]) = split /\n/, $lines[$l][$_], 2
        for 0 .. $#{ $lines[$l] };
}

use Data::Dumper;
print Dumper \@lines;
[download]

(A good example of why sometimes a C-style for loop is needed) Looks like Text::Table converts undef entries to empty string, so you don't need to do anything special to the undefs after the split.