There are several webmasters reporting that their search query report, which now shows impressions and click throughs, is showing a major drop in those impressions and click throughs as of June 2nd and 3rd. The reports come via Google Webmaster Help forums.

Yesterday, one webmaster came in and said:

Several other webmasters came in after confirming they are seeing the same thing.

Is it Google Caffeine being live related or something related to May Day or is it just a bug in Webmaster Tools?

Google has not confirmed or denied anything as of yet.

Here is a picture of a site affected by this Webmaster Tools bug named SEO Home blog:

You see that drop off? This webmaster said this has zero correlation with Google Analytics, so it must be a bug.

Forum discussion at Google Webmaster Help.

Update: Google has now confirmed this bug.