Two customs brokers and an IT worker have appeared in a Melbourne court charged over a mammoth methamphetamine haul with a street value of more than $1 billion.

Rachel Cachia, 37, Stephen Mizzi, 37, and Donovan Rodrigues, 38, briefly faced Melbourne Magistrates Court today charged with allegedly importing 1.6 tonnes of ice hidden in stereo speakers.

The trio were arrested yesterday following raids on properties in Brooklyn, Darley, Elwood, Murrumbeena and Sunshine West.

Police have seized more than $1 billion worth of ice in Melbourne. (AFP)

The haul - equal to almost 16 million drug deals - is the largest ever onshore seizure of the drug and was uncovered earlier this year, according to the Australian Federal Police.

"It's almost a quarter of the annual usage in Australia, so this will have an impact," AFP Deputy Commissioner Neil Gaughan told reporters today.

Authorities allege Cachia and Rodrigues were customs brokers who knew how to exploit the system.

They do not have security clearance and are not employed by the federal or state government.

"They are trusted insiders in the industry. They (allegedly) used their position of trust to circumvent the border controls that exist within Australia," Mr Gaughan told reporters.

"This vulnerability has been fully removed."

Three people have been arrested in relation to the bust. (Australian Federal Police)

Mr Gaughan described the pair as being "middle to high up" in the alleged drug operation.

"We feel to a certain extent that they've been used," he said.

"There's people above them, we think we know who they are, we'll keep working on the investigation to try to bring them to justice as well," Mr Gaughan said.

The haul was found by Australian Border Force officers in Melbourne in April inside a sea cargo consignment concealed in stereo speakers.

More than 35kg of heroin, with a street value of $18.5 million, was also discovered. It's the largest seizure of heroin in two years.

It's the largest seizure of ice ever on Australian shores. (Australian Federal Police)

ABF Assistant Commissioner Sharon Huey said officers were alert to "all types of creative and sophisticated methodologies" used by organised crime syndicates.

"Our officers have really seen it all. We've seen drugs in highlighter pens, hot sauce and even cowhides. Nothing surprises us," she said.

The consignment came from Thailand, but authorities believe it originated from another southeast Asian country.

An investigation by authorities in Thailand continues.

The court heard it was the trio's first time in custody.