The Tax Office has refunded $26,000 to a Melbourne couple who believe their personal details were used by thieves to lodge a fraudulent tax return.

Montmorency woman Gay Mitchell opened up her internet banking on Monday morning to pay a bill.

She navigated over to her personal savings account, where she normally had up to $800 stored.

But when she opened up the account, she found a whopping $16,000 had been transferred to her from the Australian Tax Office.

Ms Mitchell checked her husband's bank account, and found an additional $10,000 had been transferred from the ATO to him.

"My immediate thought was they've put this into my account accidentally," she said.

The couple were yet to lodge their tax return, but Ms Mitchell said they usually would not receive such a hefty refund.

She called her tax accountant and was told that a fraudster had lodged a tax return in the couple's name, and the ATO had refunded it.

"They were looking at fraudulent activity, and said their systems had been compromised, because someone was trying to lodge tax returns on our behalf," she said.

Rather than being thrilled about the enormous windfall, she is now worried that someone - who has her address and phone number - will come looking for the money.

She's also concerned that others will get caught up in the scam.

"There are a lot of very vulnerable people out there. Somewhere along the line, they've probably got people organised to ring and catch the vulnerable ones out," she said.

ATO assistant commissioner Kath Anderson said the office was investigating the reports, but that ATO systems had not been compromised.

She said the information may have been stolen from outside the ATO and recommended Ms Mitchell's accounting firm reach out to all of their clients to inform them of a breach.

It also encouraged the firm to "continue following security best practices" to reduce the risk of fraud and maintain high professional standards.

It is not known how many people have been affected by fraudsters. Radio station 3AW said it received several calls from other people who were victims in similar cases.

Ms Mitchell said her accountant was working with the ATO to rectify the incident, and for now the money had to stay in her bank account.

In a second incident, Woori Yallock woman Eloise Lowe received a $9,494.34 deposit from the Australian Tax Office on Monday - three days before she was due to lodge her tax return.

The ATO's fraud department told Ms Lowe her myGov account had been compromised.

Ms Lowe opened the account two months ago after being told it was the only way to repay a HECS debt.

Now, she's concerned about who has her personal information, and what they plan on doing next.

"I am worried as to how this can happen," she said.

"And who has my details? The people at the ATO couldn't even provide me with answers."

Ms Lowe said someone purporting to be from the ATO had left a reference number in a voicemail. When she called the office, she was asked for her name, not the reference number.

She was supplied details on how to return the money over the phone but was concerned it was part of the scam.

"That's a large sum of money," she said.

"They said to use a receipt number but there is no receipt number until you've made the payment."

A Department of Human Services spokesperson said there was no information to suggest myGov had been compromised.

DHS advised myGov users to protect their passwords and usernames for their online accounts, and to not click on links in text messages or emails purporting to be from myGov.

An ATO spokesperson said there was "definitely" an increase in the number of scams reported during tax time, but the office had "sophisticated risk models" in place to scrutinise every tax return to identify refund fraud, blatant errors and higher-risk claims. 

Fraudulent refunds could be more difficult to identify as the return appeared to be legitimate, the spokesperson said.

The ATO's client identity support centre works with victims of fraud to get their accounts "back in order".

"The most important thing to remember is never engage with someone you suspect is trying to scam you or steal your identity and don't pay them any money, even if you think the ATO paid it to you in error," the spokesperson said.

Payments to the ATO can be made electronically or in person at Australia Post.

Those who receive an unexpected payment from the ATO are urged to call the office on 13 28 61.

People who think they have been victims of identity crime can contact the ATO client identity support centre on (1800) 467 033.

With Robyn Grace