Some Isa managers might not allow the over-fifties to top up to the new limit in October, due to the “administrative nightmare” of the mid-tax year change, The Sunday Times can reveal.

The Investment Management Association (IMA), the trade body for the investment fund sector, had asked the government to consider delaying the change until April 2010, when the new limit of £10,200 will come into force for all Isa investors. The Treasury refused, but agreed not to force providers to take top-ups under the new regime.

“It is a commercial decision for each provider on whether they decide to allow further subscriptions from October 6,” HM Revenue & Customs said.

The decision has big implications for savers and investors because many are now taking out Isas in the belief that they will be able to top them up later.

Some Isa managers might decide that the cost of updating their systems, printing new literature and providing staffing to cope with a two-tier Isa system that will last for only six months, outweighs any potential benefit.

Those who have already contributed to an equity Isa this tax year and want to top up contributions could be forced to transfer to another provider who will let them invest the higher limit.

Other trade bodies, including the British Bankers’ Association, Building Societies Association and Tax Incentivised Savings Association, have lobbied the government on behalf of cash Isa providers.

Collectively, the cost to the industry could “run into millions”, sources said, and has created an “administration hiatus”. One source said: “It’s a total mess. The Treasury didn’t consult on this before they announced it and now it’s left to Isa providers to sort it all out.”

The government has, however, taken on board another proposal: anyone aged 50 by the end of the 2009-10 tax year can use the higher allowances from October 6. “Under the original proposals, someone whose 50th birthday is on April 5, 2010, would have had only 24 hours to use the additional allowance — on a day that happens to be Bank holiday Monday,” said an industry source.