Unions and employer organisations have been warned they face fines of up to $105,000 if they fail to meet new financial reporting guidelines in time.

The new federal regulator, the Registered Organisations Commission, is urging unions and employer organisations to ensure they meet strict deadlines.

Many registered organisations will need to submit a statement by September 28 disclosing details of loans they have made and donations including ones made to political parties.

Financial reports must be presented by December 31 and have been audited by an auditor who has registered with the new commission. 

Any organisations that fail to comply with new financial reporting obligations in time risk civil penalties of up to $105,000. Individuals also face potential fines of $21,000.

Registered Organisations Commissioner Mark Bielecki said it had an extensive range template financial statements and guidance notes on its website.

These were designed to streamline compliance procedures and encourage compliance.

"We are here to help registered organisations voluntarily comply with their requirements," Mr Bielecki said.

The Registered Organisations Commission was established in May to regulate and promote accountability within unions and employer associations.

"A key change for these organisations is to have an auditor registered by the ROC," Commissioner Bielecki said.

"We have proactively written to many unions and employer associations, alerting them to their financial reporting obligations.

"As a new regulator, we are committed to encouraging a culture of voluntary compliance within registered organisations and fostering their efficient management." 

Commissioner Bielecki said improvement of accountability and transparency within unions and employer organisations would increase public confidence in these institutions.

The new watchdog was set up in response to the Heydon royal commission on union governance and corruption and has sharp teeth to go after alleged offenders, including Kathy Jackson, who is facing charges for allegedly defrauding the Health Services Union of hundreds of thousands of dollars for her personal use.

The commission has powers to require people to produce documents and give evidence on oath. It can also apply for search warrants and provide protections for whistle blowers.

Mr Bielecki has previously worked in commercial litigation and has led Australian Securities and Investments Commission tax evasion investigations.

He has held a number of senior positions at ASIC, including South Australian regional commissioner and chief legal adviser. He has also worked in Sydney as the national head of PricewaterhouseCoopers legal's dispute resolution and litigation business unit.