The directive is contained in a letter from Ros Hepplewhite, the agency's chief executive, to all agency staff. It has been obtained by the Independent.
The letter, dated 5 November, says the decision not to pursue parents who are unlikely to pay was made by ministers since its initial 'take-on strategy' was drawn up.
It also confirms allegations that the agency is treating as a priority, cases where the parent with care of the children, usually the mother, is on Income Support and the father already paying maintenance.
The letter appears to undermine the impression given by ministers in the House of Commons yesterday.
Peter Lilley, Secretary of State for Social Security, said: 'Two-thirds of those we are taking on this year have been paying no benefit at all - and we have been much more successful than many people are suggesting in tracking down absent fathers who had left without any trace'.
Alistair Burt, social security minister, said he did not accept the way the agency was working had been 'totally contrary to the character envisaged'. He insisted: 'The agency is indeed pursuing those who have not paid.'
It had traced parents who would never have been traced under the previous system 'and we are indeed delivering what the public would want through the agency,' hesaid.
The instruction to target the payers and ignore the non-payers runs counter to one of the main reasons ministers gave for introducing the Child Support Agency.
The policy was sold as a way of making the irresponsible parent contribute towards the upkeep of their children because only 30 per cent of lone parents received any maintenance from the absent parent.
The Hepplewhite letter confirms the agency has changed its priorities to concentrate on paying fathers.
The Government has set the agency a target to save pounds 530m in its first year. By September, Mrs Hepplewhite told the select committee only about pounds 100m had been saved.
Urging staff not to feel discouraged or confused by the amount of publicity about absent fathers complaining about increased demands for maintenance, she wrote: 'Ministers have agreed that, once the Agency has taken on the IS (Income Support) cases where the AP (absent parent) is paying maintenance, priority will be given in those cases where the AP is not paying maintenance, to cases where there is a likelihood that a maintenance payment will be secured.'
Colin Clark, a founder of the National Campaign for Fair Maintenance, said: 'This letter shows they are still targeting those who are already paying. It shows the Government's main motivation is to get money for the Treasury, not to improve the welfare of the children.'
The letter follows another leaked memorandum from an area manager telling staff to pursue the more profitable cases. 'The name of the game is maximising the maintenance yield - don't waste a lot of time on non-profitable stuff]' it said.