Most recent figures show that 35,276 net new funds were established in the period, compared to 28,031 in the previous year.
Graeme Colley, SMSF Professionals' Association of Australia (SPAA) education and professional standards director, said the ATO overview is a positive endorsement of SMSFs at a time when regulators and government have expressed concerns about the sector.
"Although the 2011/2012 figure is the highest recorded number since these reports began in 2008, the more important factor is that the percentage increase in the number of net establishments compared with previous years appears to be slowing (a 26 per cent increase for 2012 compared to a 84 per cent increase in 2011)," he said.
At the same time, in 2012 there was a sharp decline in the number of fund wind-ups, with only 994 wind-ups compared with 5,108 in 2011 and 14,699 in 2010.
"These factors, together with increases in average SMSF balances, suggest reports that SMSFs are being oversold to unsuitable clients are being overstated," he said.
The ATO statistics also found the number of younger individuals setting up SMSFs continues to grow, with a significant increase in the number of members between the ages of 25 and 54.
"The ATO numbers show that the sector continues to perform and grow strongly in line with market expectations. While SMSFs are not suitable for everyone, there is growing evidence that suggests there is increased understanding of how they are to be used correctly," Mr Colley said.
"All the evidence suggests the right people are setting up SMSFs and, with the assistance of the appropriate professional specialists, are prudently managing their fund in a responsible way," he said.