"The adjusted NPAT (net profit after tax) decline is exaggerated because of that funding structure and the property sales," said chief executive Mark Powell.
The company has said "structural declines" in categories such as books, CDs and DVDs - as well as transitions to new product ranges - had caused the first quarter margin problems.
"There was a multiple number of issues that came together in that quarter and they were all very much short-term," said Powell.
The Red Sheds are expected to post a 4 per cent rise in same store sales for the first half, as well as a recovery in gross profit margins during the second quarter to the levels seen in the same period of the previous year, according to yesterday's trading update.
The Warehouse warned shareholders at its November annual meeting that interim profit could fall below last year's, and shares closed down 17c at $3.55 last night.
Powell said he was feeling "reasonably comfortable" about the outlook for the second half of the financial year.
"You never relax in retail (but) the trends are good coming out of Christmas," he said. "We've put a lot of hard work in and we've now had 12 quarters of (same store sales) growth in the Red Sheds and that's been pretty sustained now over three years."
Retailers also stand to benefit from rising consumer confidence, which has hit a seven-year high according to an ANZ-Roy Morgan survey released yesterday.
The Warehouse Group chairman Ted van Arkel said the board remained fully committed to the turnaround strategy that would "best navigate the ongoing changes in the retail market in order to create long-term value for our shareholders".
The company has made more than eight acquisitions and investments since late 2012, including its $65 million buy-out of Noel Leeming and its purchase of a 51 per cent stake in online sportsgear retailer Torpedo7.
Last week it announced it had entered a conditional agreement to acquire the Schooltex school uniform brand and stock from Postie Plus.