Mark Neale told the BBC that research suggested the campaign had done little to improve awareness of the protection scheme.
The FSCS guarantees up to £85,000 of deposits per saver, per authorised institution if a bank or building society goes bust.
He said that advertising may not be the best way to reach the public and hoped more information on the FSCS would appear in bank branches and on financial services literature.
The FSCS was criticised for spending £4m on an advertising campaign using cash it collects from the financial services industry annually in the form of levies.
Part of the money was used to fund a 30 second television advert on the FSCS by Wallace and Gromit creators Aardman Animation. It featured a character called Euan Mee.
Earlier this year, the FSCS defended its £4m consumer advertising campaign by comparing it to the £1.6bn the financial services sector spends annually on advertising.
