The theft now seems to have been part of a huge operation targeting government, university and military networks.
The Cisco security breach was discovered in May last year, when Russian web site SecurityLab.ru reported that it had received some of Cisco's source code from hackers.
Reports at the time suggested that as much as 800MB of code may have been stolen, with 2.5MB being posted on-line for a few days.
Investigators have taken almost a year to follow the trail to the University of Uppsala in Sweden and to an unnamed 16-year-old, who has been charged with hacking into the university's computer systems.
However, according to the New York Times, investigators have also found the trail to have many branches, revealing that the hacker, or hackers, responsible for the Cisco code theft are also behind attacks on the computer systems of leading universities, scientific labs and military installations.
These include the White Sands Missile Base in New Mexico – which has advised that a breach took place, but that the only information stolen related to weather forecasts – and various NASA sites.
The fear is that the hackers used the stolen Cisco source code to breach the security precautions on some Cisco customers' router computers, although a Cisco spokesman told the New York Times that this was not the case.
"Cisco believes that the improper publication of this information does not create increased risk to customers' networks," he said.
A worldwide maze of computers was used by the hackers to cover their tracks, says the New York Times.
The FBI and Swedish law enforcement agencies are continuing to investigate, aided by counterparts in the UK and other countries.
A British man was actually arrested in connection with the source code theft in September but, according to Reuters, no charges have been filed.