The serving officer was arrested alongside a female former Customs and Border Protection Service officer.
In a statement released by the Australian Federal Police (AFP), NSW Police, Australian Border Force, the Australian Criminal Intelligence Commission and the NSW Crime Commission, they said the border force official had been charged with multiple offences, including allegedly using his position to assist with avoiding law enforcement detection, while the female officer has also been charged with similar offences relating to her alleged conduct during the investigation.
The arrests follow dawn raids on Tuesday when more than 570 AFP officers swooped on homes and businesses across Sydney.
"Unfortunately, during this operation, we have uncovered some allegations of corrupt activity, which this syndicate exploited to try and get their drugs into the country," AFP Assistant Commissioner Neil Gaughan said on Thursday.
"We will be alleging that these persons utilised their knowledge and expertise to assist the Jomaa organised crime family bring border-controlled drugs into Australia."
The pair are two of a group of eight people arrested in Sydney and one in Dubai over their involvement in an alleged conspiracy to illegally import drugs and tobacco into Australia.
As part of Operation Astatine, a New South Wales criminal network who led drug trafficking and tobacco smuggling operations was targeted. It is alleged the network conspired to import 200 kilograms of MDMA (ecstasy) via sea cargo, smuggle 50 million cigarettes into the country, and initiate money laundering in Australia and overseas.
On Tuesday, 17 people were arrested across three countries, including two brothers of Kings Cross nightlife figure John Ibrahim, preventing about two tonnes of illicit drugs reaching Australia.
As 13 search warrants were carried out in Sydney on Tuesday, around 80 kilograms of cocaine was seized in Rosebery, and a total of $740,000 cash was found across four properties in Edmonson Park, St Peters, Hurstville and Arncliffe. An additional $2 million was uncovered by police and intelligence agencies.
Detective Superintendent Stephen Dametto from the AFP revealed that a high degree of sophistication and collaboration was necessary to uncover the dealings.
“This operation is a warning to organised crime targeting Australia that hiding on the other side of the world won’t save you. Once you are in our sights, we will focus our efforts on causing you and your predatory criminal activities as much damage as possible,” he said.
“The AFP’s international network has enabled investigators to work closely with our partners in the United Arab Emirates (and other countries) to destroy this syndicate – without their help, we would not have been able to achieve the results we have to arrest the top players in this syndicate.”
Border Protection Minister Peter Dutton said the allegations against the serving ABF officer were serious and defended the reputation of the agency.
"I want to apologise to all of the Australian Border Force officers for the alleged conduct of this officer," he told reporters in Canberra.
"This besmirches 5,500 officers who do a great job.
"It just takes one bad apple."
Mr Dutton then pointed to endemic corruption in Australia's ports "since settlement", particularly in Sydney and Melbourne.
"Our job is to weed it out," he added.