Tax Commissioner Michael D'Ascenzo said the data matching program ensured that "businesses that are doing the right thing are not disadvantaged".
If businesses are selling through these sites "you need to include this income in your activity statement and/or tax return", the ATO said. The data match will detect businesses that are under-reporting or not reporting income generated from these sources.
"The online data matching program is part of the ATO's focus on encouraging high levels of voluntary compliance and addressing the issues raised by non-compliant behaviour," Mr D'Ascenzo said.
Borg said there were two types of resellers using eBay: "One is the reseller that has superseded or oversupply of stock and tries to move it through eBay. The second is the home trader that has no infrastructure and happy to import and grey market over EBay.
"Either way it is a pain for us in a small way and probably affects retailers more than us," he said.
Data matching allows information from a variety of sources to be brought together and compiled, identifying individuals and businesses that are deliberately avoiding their tax obligations.
Anyone that makes a "voluntary disclosure will be treated fairly and benefit from significantly lower penalties", said D'Ascenzo. The ATO claimed the penalties could be reduced by 80 percent.
Businesses can make a voluntary disclosure by writing to the ATO.