Filed in the US District Court of Northern California, the suit also names the group of investors set to buy Skype from eBay.
The suit has been filed by Joltid, the company set up by Skype creators Niklas Zennström and Janus Friis, who sold the system to eBay for $2.6bn in 2005. EBay has since admitted that the move was unwise owing to the high price tag and its inability to integrate the two platforms.
This is the latest in a long running intellectual property dispute between Joltid and Skype. The firm has already filed a lawsuit against eBay in the UK.
"Joltid terminated its licence agreement with Skype as a result of breaches by Skype," said Joltid in a statement. "Skype has infringed Joltid's copyrights. Joltid will vigorously enforce its copyrights and other intellectual property rights in all of the technologies it has innovated."
According to the filing, Friis and Zennström retained some rights to the software after the sale to eBay, in particular a piece of the peer-to-peer communication system called 'Global Index', which it licensed back to Skype.
However, the suit alleges that Skype has shown the Global Index source code to third parties and altered it without permission.
Joltid is seeking an injunction from the courts and reckons that damages are racking up at a rate of $AU86m a day, which would amount to a hefty payout if the judge agrees.
It was reported in April that Friis and Zennström were looking to raise around $1bn (£605m) in private equity funding to buy their invention back from eBay.
The legal action could have negative consequences for eBay's sale of the majority of Skype to a consortium of investors, and could even see the end of Skype completely.