The book retailer said the loss amounted to 59 cents per share in its latest quarter compared with a loss of $5.5 million or 22 cents per share a year ago.
Revenue totalled $171.5 million, down from $186.6 million.
"The decrease was primarily the result of the decline in hit-related book sales, higher inventory markdown as well as intentionally higher selling and administrative expenses compared to last year," the company said in a statement.
Excluding revenue from the two hit trilogies, Indigo said revenue was down 1.3 per cent compared with a year ago.
On a same-store basis, Indigo and Chapters superstores sales were down 7.3 per cent, while Coles and IndigoSpirit small-format stores were down 13.1 per cent.
Excluding the big trilogies, same-store sales were down 1.6 per cent at the superstores and increased 1.1 per cent at the small-format stores.
Indigo operates under several banners including Indigo Books and Music, Chapters, the World's Biggest Bookstore and Coles.