Yesterday we reported that Google Webmaster Tools Search Queries Report Impression & Click Drops. This morning, Google confirmed the bug.
JohnMu at 6:30am wrote:
Thanks for posting! We have been analyzing the situation and found the problem. The data should be visible within a week or so.
So if you are affected by this, you should be okay within a week. Google also posted it as a known issue:
The search query data shown in Webmaster Tools for the month of June may not be complete for some sites at the moment. We are aware of this issue and are looking into it; you do not need to take any action. We hope to have the full data shown again in the near future. This will have no effect on your site's performance in search results. Thank you for your patience.
Forum discussion continued at Google Webmaster Help.