POI should be able to open both protected xls files (using org.apache.poi.hssf.record.crypt) and protected xlsx files (using org.apache.poi.poifs.crypt). Have you tried these?
If you’re using HSSF (for a xls file), you need to set the password before opening the file. You do this with a call to:
org.apache.poi.hssf.record.crypto.Biff8EncryptionKey.setCurrentUserPassword(password);
After that, HSSF should be able to open your file.
For XSSF, you want something like:
POIFSFileSystem fs = new POIFSFileSystem(new FileInputStream("protect.xlsx"));
EncryptionInfo info = new EncryptionInfo(fs);
Decryptor d = Decryptor.getInstance(info);
d.verifyPassword(Decryptor.DEFAULT_PASSWORD);
XSSFWorkbook wb = new XSSFWorkbook(d.getDataStream(fs));
Full details are given on the POI Encryption documentation page