Australian police have charged a teenage boy for allegedly making threats on social media that led to Sydney's iconic Opera House being evacuated last week in a security scare.

The 17-year-old boy made the threat last Thursday morning through an unspecified social media account, New South Wales state police said, causing the harbour-front concert hall to be cleared of visitors and searched in a 90-minute lockdown.

A Sydney harbour wharf in the suburb of Manly was also searched by officers after reports that the threats may have come from someone on a ferry that links the two locations.

The lockdown was lifted after police found nothing of interest at either site.

The boy was arrested on Monday and charged with false representation resulting in a police investigation. He is due to appear in a children's court in late February.

Australia lifted its terror threat alert level to high in September 2014, introduced new national security laws and conducted a string of counter-terrorism raids amid concerns of attacks by individuals inspired by organisations such as the Islamic State group.

It has also cracked down on Australians attempting to travel to conflict zones including Syria and Iraq.

In January last year, an unattended package left on a Sydney ferry sparked a lockdown of the city harbourfront, in what turned out to be a false alarm.