The Bureau (BOM) and the Australian National University (ANU) will implement two interoperable high-performance grid computing systems in Melbourne and Canberra respectively.
The ANU supercomputer will consist of some 1,500 Sun Blade server nodes based on Intel Nehalem processors.
The BOM site will include additional 1,000-plus nodes to support weather forecasting - including for cyclones and other severe weather and emergency management, such as the tsunami warning system.
Sun said it implemented a dual rail Infiniband solution at BOM, which offers multiple, independent, high-speed network connections on each blade to a fully non-blocking Infiniband fabric.
BOM will implement six racks of the extreme high-density blades in its new data centre, according to its CIO Phil Tannenbaum.
Both BOM and ANU will also run the Sun HPC software, Linux Edition, stack.
"This implementation will position the Bureau as the world's first major weather service to operate within an open source environment," Tannenbaum said.
"It's a move away from where we've traditionally been operating and we believe the Sun infrastructure will benefit our operational systems, as well as our research and development users.
"We anticipated moving to open source supercomputing for the next generation, and are pleased to have the opportunity to adopt it in 2009."
It is also expected the new supercomputer will "provide a peak computational facility for the Australian research community", according to Sun.
In particular, BOM and ANU, along with the CSIRO and other Australian universities will collaborate through the environments to develop and improve weather and climate forecasting models and applications, using the Australian Community Climate and Earth System Simulator.
The head of ANU's supercomputing facility, Dr Ben Evans, said the new system will be among the world's top 30 HPC systems.
The $30 million joint investment will be made over a four-year period.