The letters are being sent to parents who have used the Child Support Agency (CSA), warning that the non-resident parent will pay a 20% fee on their payments, with the other parent losing 4% of the money received.
The changes come as a result of the CSA being abolished and replaced with the Child Maintenance Service (CMS), and work and pensions minister Steve Webb said it would provide an incentive for parents to reach an agreement.
The letters inform parents that the state-administered system will involve a £20 charge to set up, with continuing charges on payments.
The non-resident parent, usually the father, will pay 20% on top of their payments, so for every £100 they pay £120, while the parent looking after the child would receive only £96 as a result of the 4% charge on them.
But the Department for Work and Pensions (DWP) stressed that parents could avoid the charges by agreeing to pay each other directly, bypassing the state-run system.
Mr Webb told BBC Radio 4's Today programme: "The goal here is to get more child maintenance for more children and to make the default for parents, even though they have separated, to sort things out for themselves rather than rely on the state bureaucracy."
Parents could pay a £20 charge to use the system to calculate payments, but then pay each other directly to avoid the continuing levies, Mr Webb said.
"If we don't raise a penny in charges I will be the happiest minister in government," he said.
Letters are being sent to around 50,000 parents in England, Scotland and Wales, the DWP said.
Single parent charity Gingerbread warned about the effects of the change, claiming it could lead to "unstable" arrangements.
Chief executive Fiona Weir said: "While many parents are able to agree private child maintenance arrangements, for many other parents this just isn't possible without government help.
"We're very concerned that closing CSA cases and bringing in charges may deter some parents from making new child maintenance agreements or pressure single parents into unstable arrangements, and children will lose out on vital support.
"Child maintenance can make a big difference to children, so we encourage all parents not to be put off by the charges but to seek help, if they need it, to make arrangements for their children."