The protesters rappelled down the building and hung a 2,500-square-foot sign showing an angry Ken that read "Barbie, it's over. I don't date girls that are into deforestation."
Greenpeace said Indonesian rainforests are being destroyed in part by Mattel, which uses paper products from that region to package its Barbie dolls.
Activists claim Mattel is, in essence, killing off vulnerable species, including the Sumatran Tiger.
About six people were initially arrested, but two protesters refused to come down, appearing to hold the massive banner in place. They were later arrested for trespassing.
Activists dressed as Ken hung from harnesses half way up the 15-story building.
Police had to go to the top of the building to bring them down.
Mattel responded to the protest saying, "Playing responsibly has long been an important part of Mattel's business practices."
"Over the past months, we have been in communication with Greenpeace on a variety of paper sourcing issues," Mattel said in a statement. "We are surprised and disappointed that they have taken this inflammatory approach, considering the open channels of communications we've established. We will continue to assess our paper sourcing and packaging improvements as we move forward."