Is it true that the US supported genocide in Indonesia in the 60s?

I have seen this claim made, for example, by Noam Chomsky, but I know little about Indonesia and have no context for judging. The claim is that during the 1960s, there was a revolution in Indonesia; the victors slaughtered hundreds of thousands of people. In response, the US praised the new government in Indonesia because it was pro-US and pro-business. They ignored the m murders and claimed that what killings occurred were against communists. The US media also ignored the m murders and repeated the official US government line. Is this true? An intelligent, non-ideological reply with sources (web or printed) will be most welcome.