The agency says the decline followed a 2.8 per cent decrease in the first quarter.
In the non-financial sector, operating profits fell 3.9 per cent to $51.1 billion, following a 0.5 per cent decrease the previous quarter.
Manufacturing industries led the decline with a 16.6 per cent drop to $9.9 billion.
In the financial sector, operating profits increased by 7.6 per cent to $21.1 billion in the second quarter, following an 8.5 per cent decline in the first quarter.
Most of the second-quarter gain came from life, health and medical insurance carriers.