By Leslie Josephs 

Entrepreneur Catalina Girald credits her use of PayPal, eBay Inc.'s online-payments service, with helping fuel a surge in lingerie and swimwear orders earlier this year.

At Naja, her young San Francisco-based company, sales have increased nearly 20-fold since she began selling its products on her own website in November.

In January, Ms. Girald began using PayPal to process customers' payments for goods ordered on the site. "Our sales increased even more," she said.

But then, she said, "PayPal freaked out."

An account representative from the company emailed her May 7, informing her that PayPal was "going to apply a reserve" to her account, and temporarily withhold part of the payments from Naja's customers. It effectively halved her access to her daily revenue.

Her situation highlights the risks that heavy reliance on PayPal can pose for small merchants. Many businesses depend on PayPal--and other online payment platforms--because the services offer consumers and businesses a level of confidence and security. It is up to PayPal, however, to size up the risk of fraud. And some entrepreneurs say its precautions are too heavy-handed.

In Naja's case, it can take 45 days to make and ship some products, such as embroidered bustiers, to San Francisco, and then on to customers, from a factory Ms. Girald owns in her native Medellín, Colombia. The transactions were considered a "presale" because the items hadn't been produced yet.

Her company ships about 50 orders of lingerie and swimwear a day, and she uses that revenue to pay the factory's 16 seamstresses. In addition, she recently hired 10 contractors to handle her new order volume.

In its emailed notice, which was reviewed by The Wall Street Journal, PayPal told Ms. Girald that, "During a recent review, we determined that there may be a high level of risk associated with your PayPal account, and are going to apply a reserve to your account." It told her the first of the withheld funds would be available to her in August.

PayPal, citing its privacy policy, said it can't comment on specific cases.

But a company spokesman said presale orders, long delivery times or disputes with customers can trigger a reserve on a merchant's account. To tide them over, he said, the company offers loans that could be used to cover production costs.

"We want to avoid the situation where people buy something and don't get it," because PayPal would be on the hook for refunding that money, said Tomer Barel, PayPal's chief risk officer.

Mr. Barel declined to say how many sellers using the platform sell their products before they are made.

"PayPal's secret sauce is their ability to keep fraud low," said Gil Luria, a Los Angeles-based financial-technology analyst at Wedbush Securities. He estimates that PayPal now processes between 15% and 20% of all e-commerce payments, but he expects that to grow when the company splits off from eBay. PayPal has said it plans to list on Nasdaq in the second half of 2015.

Some merchants relying on PayPal say they need their sales revenue promptly so they can pay workers and cover other production costs, even if the products ordered haven't been produced yet.

Ms. Girald said she tried to appeal PayPal's hold on her account, but that it told her on May 16 that she had to wait 180 days before it would consider her appeal.

The question, she said, "is do you lose those sales" by not using PayPal? "Or have them on hold for three months?"

Mr. Barel said PayPal is considering other payment-processing methods, such as charging customers after their orders have shipped.

Last year, PayPal established a "crowdfunding" policy, aimed at avoiding complications when entrepreneurs raised money online to manufacture a product. The policy allows entrepreneurs to have access to the funds immediately, as long as buyers are informed that there isn't a guarantee that they will receive the product, or about other risks associated with the project.

For many small specialty merchants such as Phoenix-based Bison Made, which makes wallets and leather goods for men, PayPal is critical in making shoppers confident enough to buy online.

"Whether they trust me or not, I have no ability to steal their information" when customers pay for items via PayPal, said Sebastian Sandersius, Bison Made's founder.

Jamie Siminoff of Santa Monica, Calif., said his business, Ring, which makes camera-embedded, smartphone-connected doorbells, was an "all-PayPal shop" when he started selling his doorbells online in December 2012. At the time, he was selling the doorbells before manufacturing them.

But PayPal froze a portion of his revenues. In an August 2013 email to his company, PayPal said it set aside $25,000 as a reserve on his account and would take 10% of daily sales, releasing the money six months later.

Ring began shipping its doorbells to customers in November 2013, he said.

"They just didn't understand our business, Mr. Siminoff said of PayPal, "and, as a small business, you want to work with someone who understands your business." He now uses payments startup Stripe Inc. to process online credit-card transaction.

Ryan Fant, co-founder of New York-based Keen Home, which sells smartphone-linked heating and cooling vents, said he was buying a book of color swatches for his office when he tried to check out with his PayPal account. Mr. Fant said he thought the account was flush from preorder sales of the vents, following his appearance on the television show "Shark Tank."

He said PayPal sent him an email that it was placing a reserve on some of his revenue because of the surge in preorders after his appearance on the show.

"I was like, oh, I only have $40 [available]," he said of his account, adding that he is considering dropping PayPal.

Greg Bensinger contributed to this article.

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