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New Clipper cards will cost a small fee for adult passengers starting next month as part of an effort by public transportation officials to recover losses and tighten up fee collection.

The reloadable plastic card — which is accepted by nearly all major Bay Area transit agencies, including BART, Caltrain and AC Transit — has been available for free since its launch in June 2010 but will cost $3 for adults starting Sept. 1. Clipper cards will remain costless for youths and senior citizens.

The fee will go toward making up for the physical cost of producing a Clipper card, which is about $2.90, said John Goodwin, spokesperson for the Metropolitan Transportation Commission.

Furthermore, Goodwin said this fee will deter customers who have abused the card’s ability to go into a negative amount. Some passengers will ride on public transit to the point where the card is overdrawn and then throw the card away and simply get a new one, he said.

“That’s not a flaw in the software but a deliberate feature built into the Clipper system, so then the customer will repay that deficit,” he said. “And a lot of customers have used that feature in exactly that way.”

However, Goodwin estimates 8,000 to 10,000 Clipper cards are overdrawn in any given month, averaging $2.52 per card — resulting in a total negative amount of approximately $25,000 a month.

To promote the reuse and reloading of the card, Clipper will waive the fee for customers who sign up for the Autoload feature and get the card online, which would automatically secure funds from a credit card or bank account.

“Obviously, $3 might change or affect some people’s desire to get the card or maybe even the ability to get the card,” said Clarence Johnson, AC Transit spokesperson. “But in terms of affecting our ridership, we don’t anticipate it having much of (an impact), if at all.”

Goodwin said, despite the nominal fee, he predicts the number of Clipper cards sold will go up with students coming back to the area.

“My expectation is that as we move into late August and September, we’re going to see that number rise,” he said.

Currently, there are 1.7 million active Clipper cards, with the cards being used more than 600,000 times on an average weekday — more than 10 times the number recorded when Clipper was first launched, Goodwin said.

UC Berkeley sophomore Joe Wang, who commutes between campus and his home in San Leandro, said he hesitated because he thought the card cost money.

“Might as well get a card before they tack on a fee,” Wang said. “It’s reasonable, and it makes sense. But (the fee) is basically a trip from Berkeley to San Leandro.”

BART spokesperson Jim Allison said the Clipper card’s popularity comes from its convenience but acknowledges not everyone will get the card.

“There is certainly going to be a segment of our customers who will never want to use Clipper for personal reasons, and that’s fine,” he said.