The letter, addressed to CAG Shashi Kant Sharma, claimed that the agreement was signed following all the procedures and meeting all the mandatory criteria.
Pointing out the "lapses" and "mistakes", the Congress leader demanded a scrutiny of the CAG report, which was recently tabled in the state Assembly.
The CAG had, in a report on the Public Sector Undertakings (PSUs) for the financial year which ended in March 2016, pointed out that Kerala's interests had not been protected when the Vizhinjam project agreement was signed.
Chandy had earlier taken "full responsibility" for inking the Rs 7,525-crore multi-purpose seaport project, which had received a push after his government came to power in the state in 2011.