The website, "Better Way Alberta", was launched last month and calls for increased taxes on corporate profits instead of cuts to public services.
The labour group says it is taking the website down to avoid potential fines after checking with Elections Alberta.
Federation president Gil McGowan says the labour group is not allowed to register as a third-party advertiser under the rules.
He says Alberta's law is too restrictive and should not treat websites the same as paid advertisements.
Alberta Premier Jim Prentice is expected to call a provincial election as early as Tuesday.
"They've gone too far when they start telling advocacy groups that they have to shut down their websites," McGowan said Monday in a release.
The federation said the website has had more than 50,000 hits and its YouTube videos have been viewed more than 370,000 times.
McGowan said the federation may challenge Alberta's Elections Act on the grounds that it violates the right to free speech.
He said it appears that the law is more about muzzling groups that disagree with the government than protecting the sanctity of elections.