The loss narrowed by A$2.3 million (£1.6m) from the last year as total revenues rose by A$21 million (£14.2m) from 2011 to A$96.6 million (£65.1m), the ARU said.
In last year's report, the ARU had posted their 2011 loss as A$7.52 (£5.1m) million but that figure was increased to A$10.59 million (£7.1m) due to an accounting adjustment in reporting lower income from broadcast rights from a reduced number of Tests in the World Cup year.
Gross expenditure increased by A$17.2 million (£11.6m) as a higher currency also impacted the results.
"While revenues were higher than the previous year, so was expenditure, which was primarily due to our continued investment in the game," ARU Chairman Michael Hawker said.
"Our bottom line was also negatively impacted by A$7.5 million (£5.1m) due to the higher Australian dollar."
Revenue was boosted by a rise in sponsorship money while higher match day returns due to the increased domestic Test fixtures also contributed to the growth.
"These increases, combined with the expectation that this year's British & Irish Lions Tour will deliver substantial financial gains to Australian Rugby, provides the organisation an opportunity to better its financial position in 2013," Hawker added.
The Wallabies will host the British and Irish Lions in June and July, during which they will play three Tests.
The ARU has also received a boost from rugby sevens entering the Olympic programme for the 2016 Rio Games, with the Australian Sports Council hiking its high performance funding to the governing body by 91.2 percent to A$1.04 million (£701,000) over the 2013-14 financial year (July 1, 2013 - June 30, 2014).