http://en.wikipedia.org/wiki/Indus_script
is a writing system at all, rather than the kind of ornamentation from a pre-proto-writing stage known in several other sites of ancient civilizations. (As a reality check, we can remember that several regions of the world had elaborate empires and cities with extensive trade routes but without writing.)
Some of the controversy about this issue arises because of the extreme sensitivity of cultural heritage claims in south Asia in a region that spans a heavily militarized border. A good popular book about the nature and origin of writing systems in general, worldwide, is Visible Speech by John DeFrancis,
http://www.amazon.com/Visible-Speech-Diverse-Interactions-Co...
and the definitive compilation of international research on writing systems to the date of publication is The World's Writing Systems
http://www.amazon.com/Worlds-Writing-Systems-Peter-Daniels/d...
edited by Peter T. Daniels and William Bright and published in 1996. I haven't concluded absolutely that the Indus Valley Script could not be a writing system, but there is no sure evidence that it is, and the earliest attested writing system in a nearby region is the Brahmi script
http://en.wikipedia.org/wiki/Br%C4%81hm%C4%AB_script
that is much more recent in time (a few centuries older than the common era, that is approximately 2,300 years old) and unquestionably based on the scripts of the ancient Near East.