Experts at Kaspersky Lab, a Russian company that first identified the Flame virus, said source code was shared between the teams making the malware attacks.
Both Flame, discovered last month, and Stuxnet, revealed in 2010, attacked targets in Iran.
"What we have found is very strong evidence that Stuxnet/Duqu and Flame cyber-weapons are connected," said Alexander Gostev, chief security expert at Kaspersky.
"The new findings that reveal how the teams shared source code of at least one module in the early stages of development prove that the groups co-operated at least once."
An investigation by The New York Times has pointed to the United States as being responsible for Stuxnet, developed in cooperation with Israel to cause disruption in Iranian nuclear facilities.
There is currently no definitive evidence the United States was behind Flame, The Hill reported.
No country has as yet publicly taken responsibility for either malware attack.
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