If you try to download the top query report from Google Webmaster Tools you will be out of luck.

There is a bug that is preventing the data from being downloaded as a CSV file.

At the bottom of the top query report in Google Webmaster Tools there is a link to “Download this table.” Clicking it will in fact download a file but the file will be pretty much empty.

A Google Webmaster Help thread has reports of the issue and Googler Jonathan Simon from the Seattle office confirmed the issue, he said:

There is not ETA for a fix, but I don’t expect it to take that long.

Forum discussion at Google Webmaster Help.