The suit, which could complicate eBay's $1.9 billion sale of a 65 percent stake in Skype, was brought by Joltid Ltd, a company owned by Skype founders Niklas Zennstrom and Janus Friis.
EBay's deal to sell its majority stake valued Skype at $2.75 billion but that was well below the $3.1 billion eBay spent in acquiring Skype.
Joltid controls key peer-to-peer technology behind Skype, and the two companies are already in a legal dispute. Earlier this year, Skype had filed a claim against Joltid in the United Kingdom in a dispute over a software licensing agreement that Joltid was seeking to terminate.
Joltid had brought a counterclaim, claiming that Skype was in violation of the original agreement.
Wednesday's report also comes after Internet auction house eBay said earlier this month that it agreed to sell a 65 percent stake in Skype to a consortium including venture firm Index Ventures and private equity firm Silver Lake.
The Journal report said Joltid's suit names those investors, in addition to eBay, as defendants.
EBay officials were not immediately available, while a Skype spokesman declined to comment.
The latest report also comes after Web TV firm Joost, also owned by Zennstrom and Friis, removed its high-profile chairman Mike Volpi, who joined Index Ventures. Joost had said they were investigating Volpi's actions during his tenure as CEO and Chairman but did not elaborate.
Sources last week said Zennstrom and Friis had contacted several private equity firms in an effort to launch a bid to buy back their old business.
EBay shares dipped 1.6 percent in extended trade to $23.92 after closing at $24.32.
(Reporting by Sinead Carew and Ritsuko Ando; Editing by Tim Dobbyn, Bernard Orr)