THE biggest shipping container export out of Australia's east coast cities is thin air.

An analysis by The Weekly Times shows the major ports of Melbourne, Sydney and Brisbane ship a million empty containers a year, with food a distant second.

Huge numbers of imports have overwhelmed exports, with masses of containers unloaded and then shipped back overseas empty.

The Port of Melbourne exported 383,852 empty containers in 2010-11, ahead of food (256,000) and manufactured goods (168,000).

In 2009, the Port of Melbourne's container logistics study revealed 292,033 empty containers were exported with food on 289,841.

Australian Horticultural Exporters Association chief executive Maxwell Summers said it was "an indictment there were so many empty boxes being sent back to China or Asia that we can't fill".

"The channel-deepening project, that $900 million (spent) was about improving the port facilities for imports ... and it disadvantages exports," Mr Summers said.

The AHEA argued the channel deepening was not required as only exporters would use bigger ships.

National Farmers' Federation trade manager Charles McElhone said the figures were the "harsh reality of a dollar which has been so strong".

"Just ask our pork and horticulture guys in the more import-exposed sectors," Mr McElhone said.

Sydney Ports exported 540,823 empty containers in 2010-11. Its next biggest exports were chemicals and cereals with 49,925 and 45,452 containers respectively.

Sydney's 2010-11 trade report said the numbers were due to "the strong growth in full container imports from Asia and their subsequent empty repositioning".

In Brisbane, 98,878 empty containers were exported while 90,000 containers of food and fibre were exported in the six months to January 2012.

Meat made up 30,000 containers and cotton 26,000.

Australian Bulk Alliance chief executive Simon McNair said the Port of Melbourne's numbers were "probably a reflection of the number of (imports) and the cost of putting product in the container (to export) and the turn around time".

He warned new Victorian Government charges would add between 80 cents and $1 a tonne to the cost of exporting grain - 15-20 per cent of the trader's profit.

Industry groups, including the Australian Peak Shippers Association, have warned the port will face major bottlenecks from 2015 onwards as it reached capacity.

Increases of 50 per cent in wharfage fees and channel deepening charges are set to add $8000-$10,000 to the cost of bringing a ship into the Port of Melbourne as the Government takes an extra $75 million a year.

But the money will go into government coffers and will add $10 million to the cost of exporting Victorian farm produce, according to Victorian Farmers Federation figures.

The VFF has argued the charges are a "tax on trade".

A representative from an agricultural company, who would not be named, said he was "very upset" Agriculture Minister Peter Walsh was "not backing agriculture".

But Mr Walsh said Victoria exported a record $8 billion in farm exports last year.

 "Last July when we made the changes (to the previous Labor government's plan for new charges), the VFF claimed them as a major win for farmers," Mr Walsh said.

A spokesman for Minister for Ports, Denis Napthine, said the Victorian Government had committed to numerous port and transport projects which "far outweighs any revenue generated through the Port Licence Fee".

A Port of Melbourne spokesman said full export containers generally had 10 tonnes more goods in them than imported containers.

Many empty containers were 40-foot containers which did not suit exporters, he said.

"Empties are ... an integral part of the supply chain.

"That's why we 112,000 empties are imported (a year) specifically for Victoria's export trades."