This regex results in consecutive number not being matched like:
Not Matched : 1. 123456789 2.123456789147
Pls tell?

That's because with this regex, a match requires separator characters from the set  [- .] to be present between each three-digit group; this requirement is implied by the specification-by-example in the OP. If you want something like '123456789' to match, try:

>perl -wMstrict -le
"my @numbers = (
   '123-456-789', '123.456.789',  '123 456 789', '123456789',
   '999-999.999', '999 999-999', '999.999 999',
   '9999-999-9999', '99-999-99', '0123456789',
   '999999-999', '999.999999',
   );
 ;;
 my $diff = qr{ [-. ] }xms;
 for my $n (@numbers) {
   my $match =
     $n =~ m{ (?<! \d) \d{3} ($diff?) \d{3} \1 \d{3} (?! \d) }xms;
   print $match ? '  ' : 'NO', qq{ match: '$n'};
   }
"
   match: '123-456-789'
   match: '123.456.789'
   match: '123 456 789'
   match: '123456789'
NO match: '999-999.999'
NO match: '999 999-999'
NO match: '999.999 999'
NO match: '9999-999-9999'
NO match: '99-999-99'
NO match: '0123456789'
NO match: '999999-999'
NO match: '999.999999'
[download]

I'm puzzled by the presence of '123456789147', which you seem to want to match. This is not in accord with the negative look-around assertions in your OP. Can you please clarify: do you want any sequence of nine or more digits to match? If so, where should the separator characters '- .' fall in relation to the digits?