The Charity Commission allocated one-tenth more of its budget to staff costs in 2008/09 than it did three years earlier, according to its annual report and resource accounts, which were published last week.
The increase comes at a time when the commission's annual budget is shrinking by 5 per cent in real terms, year on year.
The amount spent on pay last year actually fell by £1m because of restructuring and a cut in staffing levels from 471 to 464.
This was offset by a £1.3m increase in spending on consultants and personnel-related costs, which include travel and subsistence, recruitment, training, conferences and seminars. Consultancy fees rose by 79 per cent to £870,000 and personnel-related costs went up by 63 per cent to almost £2.5m.
A spokeswoman for the commission attributed the rise in staff spending mainly to additional travel costs, caused by a change to how the figure is calculated, and the costs incurred by staff since teams were reorganised and put on single sites. But she stressed that the regulator was operating within its budget.
Many of the 12-strong board lived close to London, she added, and now had to travel to meetings in Wales, Liverpool and Taunton in Somerset.
Dame Suzi Leather, the commission chair, received £25,403 for travel and subsistence, compared with £19,637 the previous year. The spokeswoman said this was probably accounted for by fare increases.
"Nothing in her travel pattern has changed apart from her spending more time in London," said the spokeswoman.
Leather, who lives in Exeter and works three days a week, earned £78,000 in 2008/09. Commission chief executive Andrew Hind's pay remained in the £130,000 to £135,000 bracket.
Total staff and related costs amounted to £21.8m, or 68 per cent, of the regulator's £32.3m spending.
They amounted to £19.1m in 2005/06, £19.3m in 2006/07 and £21.5m in 2007/08 - or respectively 58 per cent, 61 per cent and 64 per cent of total spending.
The annual report says the commission registered 5,410 new charities last year and removed 7,433 inactive organisations from its register. Its contact centre answered 210,000 calls.
Fifty-seven per cent of the regulator's staff are female, 10 per cent have disabilities and 7 per cent are of black and minority ethnic origin. The civil service average is 53 per cent, 7 per cent and 9 per cent respectively.
77 per cent of charities with incomes above £10,000 filed their accounts on time, compared with 75 per cent the previous year.
The commission achieved five out of six of its key performance indicators, compared with four the previous year.
It lost three Criminal Records Bureau check certificates at its Taunton office and exposed personal data of 43 trustees from 11 charities through an "online software fault".