Prowse conceived, wrote and produced the record, an innovative musical chronicle of Auckland's 1951 waterfront dispute inspired by David Grant's book, The Big Blue.
The other finalists were Christchurch group Emeralds & Greenstone for its self-titled debut album and Mel Parsons, from the West Coast, for her debut album Over My Shoulder.
In announcing the award, Recording Industry Association of New Zealand CEO Campbell Smith said Prowse's recording was a marvellously innovative and creative account of a significant event in New Zealand's history.
"Trouble On The Waterfront revives folk music as an important medium for social commentary and is a most welcome and important contribution to the genre's growth in that area.
"Chris' recording also demonstrates superb creative values across writing, musicianship and production and we are delighted to be able to award the Folk Album Tui for 2009 to him."
On his website, Prowse describes the 155-day 1951 waterfront dispute as an epoch in New Zealand history.
"Not only was it a struggle between the left and the right, between the various forces within the union movement, but also it was a struggle that raised serious questions about the importance of civil liberties in a democracy during times of internal conflict.
"Trouble on the Waterfront explores that time through the medium of contemporary song."
The recording features some leading New Zealand singers and musicians including Bill Hickman (The Shot Band), Eva Prowse and Tessa Rain (Fly My Pretties), Andrew Delahunty (The Windy City Strugglers), songwriter and performer Arthur Baysting, and Darren Mathiassen (Hollie Smith and Rhombus).
