Google SEO Tip #92 – Why Doesn’t The Click through Data In Webmaster Tools Match What I See In Google Analytics?
Matt Cutts: That’s a good question. To give you a little perspective the Google Analytics team is separate from the Google Webmasters Tool team. In fact they are in different locations. They use different code basis. They’re really sort of completely different silos within Google. So it’s not as if a ton of data sharing goes on between those two areas of Google.
I’ll give you one example way in which they can be skewed. Google Webmaster report essentially might say, “look we know the number of impressions, we know the number of clicks, or whatever” because that’s monitoring stuff on the server side of Google. It’s basically saying ok we know how many times people saw this particular website.
So we figured it’s better to give you as good information as we have in both cases, on both situations, and then you can take that data, consider the source, and then still get good, useful, actionable information out of it.