The cards, which are available on nearly all modes of public transit in the Bay Area, including BART, San Francisco Municipal Railway, Caltrain and Alameda-Contra Costa Transit, have been exploited by people who take advantage of Clipper's "negative balance feature."
The feature, which allows a customer to take a trip even if the fare is greater than the remaining balance on the card, is triggered between 8,000-10,000 times per month, Metropolitan Transportation Commission spokesman John Goodwin said.
Rather than paying off the balance, those people simply get a new card for free, which they will be unable to do once the $3 surcharge for adult cards is implemented, Goodwin said. Cards for children and seniors will remain free, as they have been since the card program launched in June 2010.
The $3 surcharge, which does not apply to existing cards, will be waived if customers sign up for the card's autoload feature when purchasing one at www.clippercard.com.
"We want folks to reload and reuse their cards," Goodwin said.
He said another step in preventing abuse of the cards will come some time in 2013 when BART finalizes the integration of its add-fare machines with the Clipper system, which would prevent customers from leaving the BART system without having paid the full fare.
MTC officials estimate that the Clipper cards are used more than 600,000 times on an average weekday, and say the new fee will help fund the production of additional Clipper cards in the future.