The stevedoring business - a division of Australia's largest listed ports operator, Asciano - will lay off 270 of its 511 workers at the port over two years as computers take over their roles.
The Maritime Union of Australia, which represents the wharfies, accused the company of resorting to the ''mean and tricky ways'' employed during the notorious waterfront dispute in 1998, when Patrick sacked its workforce and tried to replace it with non-union labour.
The union said it was considering ''all its options'', including unprotected strike action, in an effort to reverse the decision.
It is just two months since Patrick ended a 20-month long dispute involving about 1200 wharfies that came close to turning into a Qantas-style lockout.
''The ink is not even dry on that document and we find ourselves in a position where half the workforce will have their jobs destroyed,'' the union's Sydney branch secretary, Paul McAleer, said.
''In 1998, Patricks chose to use dogs and balaclavas to destroy its workforce. If companies are going to improve productivity, you are not going to do it by sacking half your workforce.''
A Patrick worker, David Whillas, said the company had resorted to its usual ''underhanded'' tactics despite the workforce giving the productivity improvements requested over the past year.
''It's just like a stab in the back. We have just been through an EBA [enterprise bargaining agreement] - and now to turn up to work to find out you may not have a job next year,'' he said. As part of the switch to an ''automated terminal'', Asciano will invest $348 million in developing the so-called ''Knuckle'' site at the port and in new technology to allow unmanned straddle carriers, which shift containers from the docks to holding yards.
The automation of the ports operation will save Patrick $50 million a year.
Asciano's chief executive, John Mullen, said the decision to invest in Port Botany was a ''vote of confidence'' in the Patrick port division - and not evidence of a company slashing costs because of difficult times.
Mr Mullen said the automated straddle carriers ''represent the future of the industry'' with newcomer Hutchison Ports set to use the technology and DP World likely to ''head in the same direction''. Patrick has been using the technology at the Port of Brisbane since 2005.
The union said it was inevitable Patrick would automate its other container terminals in Melbourne and Fremantle. Mr Mullen admitted that ''maybe one day in the future we would automate there [in Melbourne] ... but right now we don't have any plans''.
Even before the latest decision, Mr Mullen had made clear one of his priorities was to change the work culture at Port Botany because he claimed rorting of the system by wharfies was ''endemic in the DNA''.
Asciano is beefing up its container ports operation in preparation for stiffer competition later this year when Hong Kong's Hutchison Ports breaks the duopoly Patrick has long enjoyed with DP World.
Hutchison will open a new terminal in Brisbane by the end of the year and another at Port Botany in late 2013. It is also considered likely to become the third operator in Melbourne from 2017.