The man chosen to turn around the troubled Rural Payments Agency has been thrust into a political battle over high pay after pocketing a bonus in his last job.

Tory MP Anne McIntosh has called for the Government to "root out" inappropriate bonuses after it emerged Mark Grimshaw was paid more than £5,000 at the Child Support Agency (CSA), which has been criticised with families owed £3.8 billion from absent parents.

Mr Grimshaw, who became chief executive of the Rural Payments Agency (RPA) in January 2011, earned the bonus for securing "record" child maintenance collections. But Miss McIntosh insisted some payments were "simply not warranted".

Miss McIntosh raised the case amid political fury over bonuses which forced Royal Bank of Scotland chief executive Steven Hester to turn his down.

"At a time of austerity, when the Prime Minister's asking for pay restraint, why are we paying these generous bonuses?" she asked, adding that any performance-related payments should be open and transparent.

It recently emerged thousands of child maintenance claims are having to be processed by hand because of computer problems at the CSA, while in his new job Mr Grimshaw is charged with turning round the RPA after years of trouble endured by farmers due European subsidies.

A Child Maintenance and Enforcement Commission spokesman, of which the Child Support Agency is a division, said the bonus was awarded because Mr Grimshaw "helped secure record child maintenance collections despite the well-known deficiencies of the CSA's systems".

The RPA, which administers around £2 billion of grants a year, has hit its first target of the year, raising hopes the body has finally turned a corner.

The single farm payment was launched in 2005 with the promise that bundling a number of subsidies into one would see hard-pressed farmers get their money quicker.

But ill-equipped computer systems were blamed for payments being made late, while over and under-payments were a recurring problem.

The single payment scheme faces another upheaval, though, when the Common Agricultural Policy is reformed after 2013.

The RPA says it has improved communication with farmers, saying those who have yet to be paid get clear reasons why there is a delay. The issue was raised in the House of Commons last week.

Miss McIntosh asked Chief Secretary to the Treasury Danny Alexander if he would "extend his review to cover the culture of bonus payments that has built up".

She said: "Is he aware, for example, that the chief executive officer of the Rural Payments Agency is being paid a bonus for the work that he did while presiding over the Child Support Agency? Will he root out this culture of bonus payments for poor performance, when they are simply not warranted?"

The minister responded that the Government has "substantially reduced the bonus payments to many individuals" but that it needs to "ensure that good performance is properly recognised at all levels in the public sector".