The charges are expected to hit private investors from the middle of the year, when the Stock Exchange moves to a five-day settlement period.
Although brokers with private clients are unwilling to forecast exactly the new costs, they concede that dealing will become more expensive.
Mike Jones, technical service director at Capel-Cure Myers, said: "Brokers will analyse their business and see that clients who keep share certificates are costing them more. In turn, they will start charging them more. Differential pricing will be introduced."
The higher costs follow the introduction of the Crest electronic settlement system last year.
Currently, there is a rolling 10-day period in which investors who buy equities are required to ensure that payment is made by the 10th day after dealing.
Many private investors like to keep share certificates. But brokers say the administrative costs associated with certificates and transfer forms are burdensome.
The alternative is nominee accounts - where the broker holds the shares in the firm's name rather than that of the individual client.
While the cost of doing so is cheaper, there are fears that investors could lose out in cases where holding a share directly rather than through an intermediary confers extra benefits.
For instance, shareholders in Moss Bros, the clothes firm, are entitled to a 10 per cent discount on non-sale items bought in the company's stores. Burton Group or Austin Reed shareholders can obtain similar deals.
There are also fears that nominee accounts may prove to be a way for brokers to make hidden charges. But more often, investors are simply confused by the choices confronting them.
Justin Urquhart Stewart, planning director at Barclays Bank Stockbrokers, said there was no reason for investors to panic. "The vast majority of investors who only hold a few shares and don't trade frequently are probably best staying where they are and doing nothing."
He argued that even after June, when the new five-day settlement comes into operation, they will still be able to deal on "flexible settlement periods".
They may be charged interest or a penalty for not meeting the tight settlement deadline, but it "will only be a matter of a few pence". In particular, investors who own only a few privatisation stocks or do only four or five trades a year will probably not be penalised too harshly for keeping their share certificates.
However, the more deals they do the more it starts to make sense to have a nominee account.
John Cobb, chairman of the Association of Private Client Investment Managers and Stockbrokers, said: "Logic suggests that those who deal through nominees will be charged less. I can't say how much less, but some brokers are already developing a two-tier system, for those who have certificates and those who don't."
ShareLink, the Birmingham no-frills broker, has set up a dealing service which works out cheaper for people who are in its MarketMaster nominee service. Using this service, a £5,000 share deal will cost £43 instead of £56.
Louise Allardice, head of business communication at ShareLink, said: "Being perfectly frank, it is in our economic interest to get people into nominee accounts. But what we are doing is passing some of the cost savings on to our clients."
Some brokers offer nominee accounts "free", but investors should look out for hidden charges. Others, such as Barclays, makes a charge per stock they hold in a nominee account, which works out at £37 a year for a full service for 12 stocks.
Mike Hinen is finance director of Winterflood Securities, a market-maker specialising in small investors. He said: "For any regular trader there is a good argument for going into a nominee.
"It will be cheaper and there will be less paperwork. Many offer other services, such as a regular valuation and tax calculations on dividends and capital gains."
He said that if an investor made 15 trades a year it was worth becoming a nominee.
Other brokers put the cut-off level much lower, at seven or eight deals, after which it will be worthwhile operating through a nominee. The alternative is to negotiate a discount on dealing - but that is subject to regular trading and at high volumes.Reuse content