Two men alleged to be key organisers in a Mexican crime syndicate operating in Melbourne have been arrested after police seized 300 kilograms of cocaine.

Police alleged the drugs, which had an estimated street value of $105 million, were hidden in a shipment of cacao powder and coffee sent by air to Melbourne last week.

Earlier this month, a 34-year-old Mexican man arriving from Los Angeles was detained at Melbourne Airport after allegedly being found in possession of a small amount of cocaine.

Further investigations by the Victorian Joint Organised Crime Taskforce led authorities to a logistics company in Altona, in Melbourne's south-west, where they found the cocaine.

Raids were also conducted at properties in Port Melbourne and Balaclava on Wednesday, which resulted in the arrest of a 33-year-old Mexican man.

It was a great result to keep the drugs off the street, Assistant Commissioner Fontana said. ( Supplied: AFP )

Both men were charged with importing a commercial quantity of drugs and were remanded in custody after appearing at the Melbourne Magistrates' Court.

They are due back in court next March.

Australian Federal Police (AFP) Commander John Beveridge said the pair were allegedly key organisers in the cocaine importation syndicate.

"During this investigation we used the AFP International Network and worked closely with officers at the newly opened AFP post in Mexico,'' Commander Beveridge said.

"We were able to obtain intelligence on this organised criminal syndicate from the source and trace their activities across the globe.''

The drugs were found in boxes of coffee and cacao products. ( Supplied: AFP )

Victoria Police Assistant Commissioner Steve Fontana said it was a great result to stop the cocaine from hitting the streets.

"Drugs are not harmless, they are not safe and they have had deadly consequences for some people,'' Assistant Commissioner Fontana said.

The Victorian Joint Organised Crime Taskforce involves officers from the AFP, Australian Border Force, Victoria Police and the Australian Criminal Intelligence Commission.