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The OpenCV tiff handling is quite basic (compared to what you can store in a TIFF file) - however normally it should be able to read 16 bit TIFF files.
Anyway, if you are having problems with the imread function, you better use libtiff to handle these images. It can handle any bit depth, any number of channels and any kind of data.
I already wrote a post about reading TIFF files with Libtiff and Opencv: http://answers.opencv.org/question/86621/reading-geo-tiff/#86740
