Mark Zuckerberg admitted that the Facebook’s games ecosystem “is not doing as well as I’d like” today on Facebook’s Q3 earnings call, though he said it is growing overall.

Payments revenue from social game giant Zynga dropped 20 percent for Facebook compared to Q3 2011. In total, Zynga made up 43 percent of Facebook’s Payments revenue this quarter and just 7 percent of Facebook’s total revenue (including Zynga’s ad spend). This is down significantly from previous quarters where Zynga has made up as much as 63 percent of Payments revenue (last year) and 12 percent of total revenues (at the point of Facebook’s IPO).

Even so, Zuckerberg says the games ecosystem as a whole is growing with revenues from other game developers increasing 40 percent over the last year since Payments was made mandatory for game developers. Payments (and other fees) revenue for Q3 was up year on year almost 13 percent from $156 million to $176 million.

Zynga’s Q3 earnings call is scheduled for Wednesday. Reports today indicate a large number of its employees were laid off earlier this morning and its Boston studio was closed.