If you were hit by the Penguin update, you should probably use Google’s new Link Disavow tool, particularly if you can’t get bad links removed. That’s the message we’re getting from Google’s Matt Cutts.

Cutts and Google really emphasized that most people should not use the tool, and basically painted the tool as a last resort kind of thing, but Danny Sullivan has posted a Q&A session with Cutts in which he says:

“The post [Google’s announcement post last week] says anyone with an unnatural link warning. It also mentions anyone hit by Penguin, but I keep getting asked about this. I’m going to reiterate that if you were hit by Penguin and know or think you have bad links, you should probably use this too.” Emphasis ours.

Here’s the exact text from the original post:

“If your site was affected by the Penguin algorithm update and you believe it might be because you built spammy or low-quality links to your site, you may want to look at your site’s backlinks and disavow links that are the result of link schemes that violate Google’s guidelines.”

Sullivan asked Cutts how long it will take for sites to see improvement, asking if sites may have to take into account the time it takes for Google to push another Penguin update. Google had initially indicated that it could be a matter of weeks, but here, Cutts admits that it could be as long as months.

“It can definitely take some time, and potentially months,” Cutts is quoted as saying. “There’s a time delay for data to be baked into the index. Then there can also be the time delay after that for data to be refreshed in various algorithms.”

As Penguin victims know, webmasters can be waiting quite a while for Google to roll out a refresh.

Even though Cutts says that you should probably use the tool if you were hit by Penguin, don’t take that to mean that it will do any good if you use it without actually trying to get links removed first. He also told Sullivan that you shouldn’t count on it working if Google doesn’t see any links actually taken down off the web.

While the tool is something that some webmasters and SEOs have wanted for a long time, it may not be the silver bullet that they had really been looking for. Google even acknowledged in its original post about the tool that it might not ignore some links you tell it to.

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