MEGAN only imports BIOM1 format correctly. This format is a JSON-based format, in comparison to BIOM2, which is a HDF5-based format.
If you are trying to import a BIOM file and get this type of error message, your file was most likely saved in BIOM2 format:
To check your file, look at the first line. If the line starts with HDF5, you will have to convert your file into BIOM1 format.
An explanation on how to convert BIOM files between the two versions is given at biom-format.org.