Mothers and fathers who turn to the Child Maintenance Service (CMS) to collect and pay settlements face losing significant sums of cash.
Non-resident parents will be forced to hand over 20 per cent on top of the payments and the other parent will lose 4 per cent of the money received.
Applications to use the new system will cost £20 and absent parents who have to be pursued through the courts or have maintenance deducted from their earnings will also be hit by extra charges of up to £300.
Ministers insist the reforms are being introduced to encourage parents to work together to make their own arrangements, freeing up the service so it can focus on the most challenging cases, but critics fear it will put pressure on parents to accept unsuitable arrangements.
Letters were sent to around 50,000 parents in England, Scotland and Wales earlier this year warning them about the changes as the CMS replaces the Child Support Agency, which is being phased out over the next three years.
Parents that come to an agreement without CMS intervention will be able to use a Direct Pay service to exchange payments – a system 39 per cent of parents are using, according to the Department for Work and Pensions.
Work and Pensions Minister Steve Webb said: “Reform of the old broken system was absolutely necessary and today marks a key milestone in the Government’s essential reform of the child maintenance system in Great Britain.
“The old CSA was just not fit for purpose – it spent £503m in one year to transfer £1.1bn of maintenance and left more than 50 per cent of children living in separated families with no effective financial arrangement in place at all.
“The new system is helping more couples to work together to ensure the best outcomes for their children.
“We know that children do better when parents work together, even after separation, and I am very encouraged that the new child maintenance system is already making this a reality for thousands of families.”