Unfortunately this is mentioned in upgrade notes to MySQL 5.6
Incompatible change: For TIME, DATETIME, and TIMESTAMP columns, the storage required for tables created before MySQL 5.6.4 differs from storage required for tables created in 5.6.4 and later. This is due to a change in 5.6.4 that permits these temporal types to have a fractional part. After upgrading from MySQL 5.5 to MySQL 5.6.4 or later, it is recommended that you also upgrade from MySQL 5.5 to MySQL 5.6 TIME, DATETIME, and TIMESTAMP types. ALTER TABLE currently allows the creation of tables containing temporal columns in both MySQL 5.5 and MySQL 5.6.4 (or later) binary format but this makes it more difficult to recreate tables in cases where .frm files are not available. Additionally, as of MySQL 5.6.4, the aforementioned temporal types are more space efficient. For more information about changes to temporal types in MySQL 5.6.4, see the section called “ Storage Requirements for Date and Time Types ”.
There is also mentioned workaround to get from 5.5
to 5.6
using Memory storage, but it says nothing about downgrading.
Only advice available is from http://bugs.mysql.com/bug.php?id=71381.
The only option I see here is to do a dump on the 5.6 of the tables with these temporal columns on 5.6 and then importing them in 5.5