By Juliet Chung and Vipal Monga 

Several global banks have begun charging large customers to deposit their money in euros, a rare move that could have costly implications for investors and companies that do business on the Continent.

The actions are driven by policies from the European Central Bank, which in June became the largest central bank to impose a negative interest rate on deposits--meaning banks are paying to park their money with the ECB. The effort is designed to encourage banks to instead use that money to lend. When the ECB dropped those rates further in September, some banks started pushing those costs--or costs related to the rate cuts--onto customers.

Now, instead of paying customers interest on their euro accounts as they have done traditionally, some banks have started charging them. Bank of New York Mellon Corp. recently started charging 0.2% on euro deposits, the bank said Friday, and Goldman Sachs Group Inc. and J.P. Morgan Chase & Co. have also started charging clients, according to people familiar with the matter.

Meanwhile, Credit Suisse Group AG has told customers it will pass along negative interest rates on all currencies in which they apply, people familiar with the matter said, and has started charging on euro deposits.

The reversal is the most sweeping of its kind that many bankers and their clients say they can recall. The clients most immediately affected are investment firms, such as hedge funds and mutual-fund companies. Multinational corporations with sizable operations in Europe could also face additional costs, according to people familiar with the matter.

HSBC Holdings PLC will soon start charging customers with more than roughly 10 million euros in deposits, according to a person familiar with the matter. The move is intended to discourage a flood of deposits from institutional investors fleeing competitors that have already started levying charges on euro deposits, the person said. An HSBC spokesman said Friday the bank was "monitoring the situation."

Several bankers said the changing regulatory landscape has made it harder to eat the cost, as they might have in the past. In 2011, BNY Mellon disclosed a move to charge some of its U.S. depositors for holding their cash, after investors poured money into the bank to escape gyrations in the market. The bank later aborted the plan.

A BNY Mellon spokesman said the 2011 situation "resolved itself" as deposit levels shrank. "The current euro situation is much more enduring and is likely to be the norm for some time," he said.

The latest move by the banks is notable because so many of them are taking the same step, giving customers fewer options for moving their money. Several people familiar with the matter said the fees could vary depending on the client and the bank.

"As we go through this period of low-interest rates in the Eurozone, our expectation is this is going to linger for a long time," said Peter Yi, head of short duration fixed income at Chicago-based trust bank Northern Trust Corp. "This isn't something that's going to go away in the next year."

Mutual-fund firm Vanguard Group confirmed they are being charged for their euro balances. "That is being passed on," said Vanguard spokesman David Hoffman. "It's very recent."

He declined to say which banks are instituting the charge, or detail the firm's euro cash exposure.

The new charges are setting off a search by some clients to try to avoid or minimize fees. Investors and bankers say some are moving their balances into cash-like instruments such as money-market funds or repurchase agreements, also known as "repos," which are short-term loans backed by collateral. Other clients are looking for banks where they can park cash without getting charged.

The BNY Mellon spokesman said the bank was working with clients who were looking for alternatives to cash deposits to find investment opportunities.

In an interview on Friday, BNY Mellon Chief Financial Officer Todd Gibbons said the firm expects the fees to be imposed across the industry. He said 15% of BNY Mellon's deposits are euro-dominated and that he expects most of the affected clients to be "savers on the institutional side," including financial-services firms, corporations and pension funds.

BNY Mellon began charging clients 0.2% on euro deposits starting Oct. 1, according to a memo sent to clients. Mr. Gibbons also discussed the charge on an earnings call Friday.

The charges highlight the divergent paths central banks in the U.S. and Europe are taking. Although the Federal Reserve has kept interest rates low for years, it continues to pay banks on excess deposits and has signaled it hopes to raise rates relatively soon.

The fees also underscore challenges institutional depositors such as hedge funds, mutual funds and corporations may face going forward in finding a welcome haven for their deposits. Banks are forced to set aside more capital against deposits under new banking rules yet have difficulty earning any return on that cash, making such deposits unattractive.

Relationships between banks' prime brokerage businesses, which execute and finance trades for clients, have already come under pressure as banks have started squeezing their clients for more profits.

In positive interest-rate environments, banks typically earn interest on client cash and pass part of that return on to their depositors. On euro deposits, banks can get paid the ECB's overnight deposit rate; the rate on benchmarks like the Euro Overnight Index Average, or Eonia, that trade and tend to trend with the ECB's interest rates; or yield on other investments.

The ECB in early September lowered its rate deeper into negative territory, to -0.2% from -0.1%. The Eonia went negative for the first time in late August.

Not all big banks are following suit. Deutsche Bank AG had not started levying charges on euro deposits as of Friday, according to people familiar with the matter.

State Street Corp. said in a statement Friday it hadn't yet started charging on euro deposits but that it had told clients it might do so in the future. "Continued persistence or deterioration of the current rate environment may require that we take action consistent with prudent financial management," the statement said.

Anthony Carfang at Treasury Strategies, a Chicago-based consulting firm, said highly visible negative rates made such charges more palatable than they may have been in the past. "This looks like a pass-through," he said. "That makes it a lot more acceptable in the customer's mind."

Max Colchester and Daniel Huang contributed to this article.

Write to Juliet Chung at juliet.chung@wsj.com and Vipal Monga at vipal.monga@wsj.com

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