Charities that run chains of academy schools are using public funds to pay senior staff six-figure salaries, with some on £240,000 or more.

The Guardian analysed the most recent annual reports of five major chains, each of which receives tens of millions of pounds from the government each year.

The reports, which are for the year ended 31 August 2010, show three chains – Ark Schools, Harris Federation and the United Learning Trust – awarded already high-earning staff performance-related bonuses, or increased their pension, salary and bonus packages from the previous year.

Brian Lightman, general secretary of the Association of School and College Leaders, said the figures were "astonishing in the current economic climate" and warned that public funds may be being channelled into the pockets of individuals and away from the needs of pupils.

The accounts show that Sir Bruce Liddington, the director general of the E-Act chain, earned £280,017 in salary, pension contributions and bonuses. He was appointed in March 2009 and was paid £154,583 for his first six months of work.

E-Act increased the number of academies it runs from seven to 11 over the year to August 2010. The charity now runs 14, including a free school.

A director of the Harris Federation earned £243,027 – a rise of £26,411 on the year before. The chain boosted its number of academies from seven to nine over the year, and now runs 13 in south London.

One member of staff at the Academies Enterprise Trust earned between £200,000 and £209,999. No member of staff had been in this pay bracket the previous year, the accounts show. The chain grew from three to six academies between August 2009 and the following year.

The United Learning Trust paid one of its staff between £180,000 and £190,000 in gross salary and bonuses. The chain increased the number of its academies from 14 to 17 between August 2009 and the following year.

The chains would not reveal, with the exception of Liddington, which senior staff had received the most generous packages. Senior staff include finance and education directors of the chains, as well as academy headteachers. The packages tend to include salary, bonuses and, in some cases, pension contributions.

Academies receive a similar amount from the Department for Education as do state schools that work with local authorities. However, academies are given extra for the services that councils would otherwise provide and they do not have to adhere to rules governing the pay and conditions of senior staff, as state schools working with local authorities do.

The maximum salary of a headteacher at a state school under local authority control is between £79,835 and £112,181. Only a headteacher in a large inner London secondary school would be eligible for the higher sum.

The accounts show that another member of staff at the United Learning Trust earned between £150,000 and £160,000, while three at Ark Schools were paid between £140,000 and £150,000. No staff at either chain were in these pay brackets the year before. Four employees of Harris Federation earned between £130,000 and £140,000, compared with just one the year before.

Ark Schools said it awarded financial incentives to all staff based on the performance of pupils. A spokeswoman said the chain negotiated packages of performance-related pay with staff. "We pay competitive rates, but we don't overpay," she said.

The chain grew from six academies to eight between August 2009 and the following year. In addition, it created a new secondary school for an existing academy and recruited an extra principal.

The United Learning Trust and Harris Federation said they had awarded pay rises in accordance with agreements with trade unions and had more staff because both chains had grown.

The Academies Enterprise Trust said the financial packages of its staff reflected its expansion and the fact that some staff had received payments from their predecessor schools for the previous year's performance.

However, Lisa Nandy, a Labour MP for Wigan who is on the cross-party education select committee, said the accounts showed academies paid "staggeringly high amounts" to those at the top, and warned that they were underpaying some junior staff because they were exempt from the pay and condition rules of other state schools.

Lightman said he feared that "in a time of very limited resources, disproportionate amounts of money were being spent on a small number of people". He said: "This will take important funds away from the classroom."

In numbers

£207,017

Amount paid to Sir Bruce Liddington, director-general of the E-Act chain of 14 schools and academies. He earned £154,583 for just his first six months of work in 2009

£243,027

Earned by a director of the Harris Federation chain, a £26,411 increase on his salary the year before. The group runs 13 academies

£112,181

The maximum salary of a headteacher at a state school under local authority control. The minimum salary for heads of smaller schools is £79,835