Microsoft Australia has paid an extra $39 million in tax following an ATO audit.

Microsoft agreed late last year to resolve matters with the ATO after a company audit covering the years 2010 to 2013.

As part of the settlement, Microsoft paid an additional $39 million in previous tax liabilities, raising its total 2017 tax bill to $87.3 million on taxable income of $130.5 million.

The previous year, Microsoft had paid $36.4 million on taxable income of $92.3 million.

Microsoft, Apple and Google faced a senate committee investigating tax minimisation strategies in 2015.

At the hearing, Microsoft vice president of worldwide tax Bill Sample conceded that a big chunk of the company’s Australian revenue was booked by an affiliate business in Singapore.

“The products and services we sell to Australian customers are sold by the Singapore group, and the sales people are primarily located in Singapore,” Mr Sample said at the time.

In the 2014 financial year, Microsoft's Australian product and customer service revenue was around $2 billion – all of which was booked and taxed in Singapore.

The ATO gained new powers in 2016 to ensure global companies return their sales to Australia.

Microsoft Australia says a significant amount of revenue has since been repatriated.

The company’s Australian revenue increased by around 45 per cent to $1.05 billion in the financial year ending 30 June 2017.

Facebook and Google stated after the senate sessions that they would similar efforts to ensure money made in Australia was taxed appropriately.