Police have backed the federal government's controversial metadata laws, saying they were able to use phone data to quickly clear the parents of Brisbane boy Daniel Morcombe of suspicion in his disappearance.

As the nation's law enforcement and intelligence agencies seek to explain the importance of making sure such data is kept by service providers, Australian Federal Police counterterrorism chief Neil Gaughan has told Fairfax Media that it can be used to exonerate the innocent as well as to pursue the guilty.

Beneft: Police were able to use metadata to determine the parents of Daniel Morcombe played no part in his disappearance. Credit:Andy Zakeli

His comments came after the Abbott government last week unveiled the plan to force phone and internet companies to keep metadata – information such as the time, duration and recipient of phone calls, text messages and emails – for at least two years in case it is needed for criminal or intelligence investigations.

The legislation has raised concerns that it could lead to unprecedented surveillance over ordinary Australians, giving a wide range of authorities the ability to access the data. Telecommunications companies have also voiced criticism, saying unless the government agrees to pay for the scheme, consumers will face higher internet bills, due to the cost of storing the data.