Thousands of people who bought into low-risk savings certificates with the government’s savings arm have been short-changed due to failings in its computer system, The Sunday Times can reveal.

About 15,000 savers who cashed in index-linked savings certificates from Treasury-backed National Savings & Investments (NS&I) before maturity and not on an annual anniversary date have received less in interest than they should have.

The certificates are designed to beat inflation, as measured by the retail prices index (RPI), by a margin of interest — 1% at present. In the event of deflation, only the interest is received. However, NS&I’s computer system has offset savers’ interest against the negative rate of inflation, incorrectly reducing the payouts.

RPI peaked at 5% in September but went negative in March — making the certificates far less attractive. Gill Stephens, NS&I spokeswoman, said the provider’s IT system had been unable to cope with a prolonged period of deflation: RPI was –0.4% in March, –1.2% in April and –1.1% in May.

“A number of our customers who cashed in their certificates between anniversary dates have received lower-than-expected payments,” she said. “This is now being rectified and we will be making a retrospective repayment to anyone affected.”

Gordon Huckstep, 63, from Winchmore Hill, north London, was shocked to discover that the interest added was less than the guaranteed 1% advertised when he cashed in his NS&I index-linked savings certificates earlier this year. After twice writing to NS&I, he received a letter agreeing to pay £187 — the amount of interest deducted — as well as a further £50 compensation.

Huckstep, who is retired, said: “I couldn’t find anything in the terms that allowed for this process of offsetting. It’s taken three or four months to sort out.”

Money has also been inundated with letters from readers hitting out at the way in which NS&I claims the certificates “always stay ahead of inflation”. Savers can invest between £100 and £15,000 in each issue over either three or five years and NS&I guarantees that they will never get back less than they invested, even if they cash in the certificates early.

A fixed rate of interest (1% on current issues) and index-linking is applied once a year. However, if inflation has turned negative from one anniversary to the next, no index-linking is applied. That means that someone who invested in March last year would have received no index-linking come this March, despite inflation being in positive territory for 11 months of that year.

Some savers who requested a valuation statement part-way through their policy’s year have seen the value of their savings fall as index-linking, previously calculated due to positive RPI, is clawed back.

Ronald Porter, 59, from Sevenoaks, Kent, saw his holdings worth £56,000 at the start of the year drop by almost £1,000 in March. “I had the impression from the brochure that they would always hold their value, whatever happened to RPI,” he said. “The purchase price value never falls, but the interest and index-linking that the capital earns both get reduced in times of deflation. None of this is spelt out. The result is that the overall value of my investment is losing £1,000 every three months.”

NS&I conceded that interest and index-linking applied at a policy anniversary might be less than any mid-term valuation. Andrew Hagger at Moneynet.co.uk said NS&I savings certificates were “distinctly poor value” — and that far better deals could be achieved elsewhere.

If you can lock up your money, then fixed-rate bonds look a good option. Clydesdale bank and Newcastle building society pay 5% over five years, but a shorter-term bond will allow you to take advantage of expected interest rate rises. Skipton building society pays 3.85% fixed until the end of February on deposits of £500 or more, while Abbey pays 3.75% for one year on £25,000 and above.

Easy-access savings rates are also on the up. This would give you access to your savings — so that once inflation comes back you can return to index-linked savings certificates. Coventry building society launched a market-leading rate of 3.25% on its eSave account for the over-50s on Friday. Unlimited penalty-free withdrawals are allowed, although the rate is fixed for 12 months.

Four other 3%-plus easy access accounts have come on to the market in the past three weeks — 3.15% from Alliance & Leicester, Nottingham building society and Birmingham Midshires, and 3.05% from Leeds building society.