syntax error near unexpected token `fi'

You don't need the double brackets and you don't need the filename in a variant declaration. In addition you need to put the echo output in quotes.

The corrected command is below.

#!/bin/bash 
if [ -e /fms2005/Sample/CronFlag.txt ] ; then 
    echo "data file does exist"
else 
   echo "data file does not exist"
fi