Security firm Symantec caught the command using booby-trapped computers set up to watch Flame's actions.
Flame came to light after the UN's telecoms body asked for help with identifying a virus found stealing data from many PCs in the Middle East.
New analysis of Flame reveals how sophisticated the program is and gives hints about who created it.
Like many other security firms Symantec has kept an eye on Flame using so-called "honeypot" computers that report what happens when they are infected with a malicious program.
Described as a very sophisticated cyber-attack, Flame targeted countries such as Iran and Israel and sought to steal large amounts of sensitive data.
Earlier this week Symantec noticed that some Flame command and control (C&C) computers sent an urgent command to the infected PCs they were overseeing.