Google's Distinguished Engineer says that if your website is down just for a day, such as your host being down or a server transfer, there shouldn't be any negative impact to your search rankings. However, extended downtime could have an impact.
Back when Googlebot used to crawl your site once a month and rank your site accordingly during the monthly Google Dance, the sheer terror webmasters used to have that their website might be down when Googlebot came to crawl was quite common.
Fortunately, times the changed and Googlebot is regularly accessing websites on a very regular basis. However, one of the notifications in Google’s Webmaster Tools is a notice if a website is down when Google crawls.
A new Google Webmaster help video brings up the subject of what exactly happens when Googlebot can’t access the site and how that might affect Google search rankings.
According to Google’s Distinguished Engineer Matt Cutts if your website is down just for a day, such as your host being down or a server transfer, there shouldn’t be any negative impact to your search rankings. However, if the downtime is extended, such as for two weeks, it could have impact on your search rankings because Google doesn’t necessarily want to send the user to a website that they know has been down, because it provides the user with a poor user experience.
Google does make allowances for websites that are sporadically having downtime, so Googlebot will visit again 24 hours later so and see if the site is accessible.
Cutts did mention that if you think the problem isn’t with your website, go and visit the Google Webmaster help forums and see if there’s any similar posts from people having the same issue. He brought up a recent instance where Googlebot actually was having a problem on its end fetching pages when it came to accessing websites, and well many users got the notice that their website was down, a quick look at the forums showed that several people were having the exact same issue and so the problem was on Googlebot’s end.
Google does include this on Webmaster Tools notices to simply give webmasters a heads-up that there could be a problem with their websites, so it gives webmasters and alert to investigate what the problem could be. But if it is just for a short period of time and the issue resolves itself quickly, such as with a hosting companies short downtime, there is no need for concern about it affecting your Google search rankings.