You can find on the Magento Connect and download migration tool to get your job done. I think you should upgrade to 1.9.3 or 2.1
May I kindly ask you why did you decide to upgrade to 1.6 instead of 1.9 or 2.0? As far as I know, 1.6 is an outdated version and I'm not even sure enough whether the official Magento Data Migration Tool supports such kind of transfers.
In your case, you may try Cart2Cart service. And if you decide to upgrade to 2.0 in the long run, you may use this plugin.
Regards and good luck!
I've been struggling with that situation too (Because the data migration tool).
First I've made a manual upgrade on a server with the software stack requirments of that versions.
After that, I've updated to a higher version until I was able to get the code and database on 1.9.x (I didn't care about all the features and 3rdparty modules, just the core code and the database).
From them I've started to migrate using the Data MIgration Tool.