Google's site command, i.e. site:www.domain.com, is known by savvy webmasters and SEOs as not a great measurement of the total pages Google has indexed of your site.
Of course, for small sites, it works pretty well, but for really large dynamic sites, the result count presented through using a site command can be misleading or a really bad estimate.
Google's Matt Cutts said this himself back in December 2012 in video answer.
Now, Enrico Altavilla shared results of a 410 experiment he is running which gave him even less confidence in using the site command. Enrico Altavilla wrote:
You should never use the number of search results reported by Google for serious activities.
He then shares how he tried to measure this by using 410 status codes to remove pages and document the numbers returned using the site command over time.
The chart that I have attached to this post shows the current results of an on-going experiment about de-indexing resources. I had about 30,000 unimportant resources in a web site and I 410ed them, to see how Google would react to the big change.The expected results were that the quantity of those resources would decrease over time and in order to monitor this quantity I have used two of the most less reliable tools that you can think of: the "site:" search operator and the number of results reported by Google.
He says that you can "use it to monitor a trend over time but the actual numbers are almost meaningless." Most would agree with that but look at his chart:
Using Google Webmaster Tools should be way more accurate, either through the sitemap report or the index status report.
Forum discussion at Google+.