EPS is an archaic format with no transparency support. For use in InDesign resave that file as AI or PDF and place that.
FYI, if your logo was made in (for example) Illustrator, open and resave it in Illustrator (as Bob suggested) to preserve the transparency. If you don't have or don't know what program created the eps, there is a chance that the transparency has already been flattened, and resaving it as ai or pdf won't get the transparency back. It's similar to saving a Photoshop file as .ps instead of a jpeg with high compression, because jpeg can show visible artifacts, but if you already have a jpeg with visible artifacts, resaving as .ps won't help.
If the logo was (for example) created in Quark or InDesign (which sometimes is the case) and exported as eps with flattened transparency, your best bet is to find the original Quark or InDesign file that still has the live transparency and export a PDF. If you don't have access to the original file and the eps is saved with flattened transparency, you will have to edit it in something like Illustrator and recreate the transparent portions.
That is not true - you can easly export EPS with transparent backgrount. I use it all the time. I i don't think that it is archaic at all - it usually works very well without any problems - not like some .AI and .PSD files.
to r_tidt - first, try to open the EPS in illustrator (if you can) and be sure taht there really is transparency and that it is not flat image. Then export file again to EPS and check the "transparent background" option, if there is any. Second you may turn on the "import options" while placing EPS into inDesign (when you go File > place (or import - i dont know how is it in english) and you are chosing the file itself, downl bellow you can see "import option" checkbox there). There may be some options for your transparent options.
But if it really is just EPS with flat TIFF in it, you may need to recreate it as you been told.
It is true. A transparent background is not what is being discussed here.
And EPS is most certainly an archaic file format when used in an InDesign workflow. That said, when a client supplies a logo or some other artwork in EPS I’ll use it unless there’s a problem with it. In this case the file is troublesome.