Computer giant IBM continues to dominate the list - which is compiled twice a year - with a total of 232 out of the top 500 supercomputers.
Its Blue Gene/L supercomputer - used to ensure the US nuclear weapons stockpile remains safe and reliable - comes out at number one.
The Indian system - known as EKA - made it into fourth place.
The world's fastest supercomputer - BlueGene/L - has been significantly upgraded in the last six months.
It can now deliver a sustained performance of 478 trillion calculations per second (478 teraflops), nearly three times faster than any other machine on the list.
Second place went to another IBM system - a newer version of BlueGene/L known as BlueGene/P. The system, introduced this June is the first in a batch of IBM machines designed to operate at a petaflop and beyond.
Breaking the petaflop barrier - the ability to process 1,000 trillion calculations every second - has long been a key milestone in supercomputing and would allow highly detailed simulations.
For example in earthquake simulations it could show building-by-building movements of regions in earthquake zones, improving future structural designs.
India has also entered the exclusive list for the first time with a Hewlett-Packard designed system that has a performance of 117.9 teraflops.
Codenamed EKA - Sanskrit for number one - it is installed at the Computational Research Laboratories in Pune.
The system will be initially targeted at developing applications such as neural, molecular and crash simulations, and digital media animation and rendering.
"The supercomputer system will have a direct affect on the lives of Indians, espcially in areas such as earthquake and Tsunami modelling, modellings of the economy and potential for drug design," said Mr S. Ramadorai, chairman of the Computational Research Laboratories, which is a subsidiary of Indian firm Tata.
The next step for the system is to put more applications on it.
"While the ranking is important the more important thing is to keep on improving performance and applications," said Mr Ramadorai.
Third place on the top 500 list went to a new supercomputing centre based in New Mexico.
Fifth place went to another Hewlett-Packard system installed at a Swedish government agency.