Yes, i scanned ntfs partition with clamav and work fine:
1)install from repository
2)launch freshclam for update virus database
3)clamscan -r /mnt/partition -l /directory/for/log/file <--- This command scans the disk showing the output in the terminal, but also generates a log file where you can go and see, purged from all the rest, any infected files.
The infected file will not be deleted automatically, if you want check clamscan -h
I tested the program with 2 ntfs partitions, there were no viruses so I did the test with a fake virus and it worked
...and remember: wuuuuuuuuu!