The Daycare Trust says nurseries in disadvantaged areas, where lower fees are charged, are more likely to raise childcare ratios.
The charity also suggested increasing childcare ratios was risky.
The government says the changes are not compulsory and it wants to improve the quality and affordability of childcare.
It is due to make a further announcement on affordability soon.
But it had argued that relaxing the staff to child ratios for certain age groups could enable nurseries to reduce their costs and therefore be more affordable, and has proposed allowing the ratio of staff to children aged two to three to be raised from one to four, to one to six.
But the charity, which recently merged with the Family and Parenting Institute, says plans to alter ratios are likely to "exacerbate differences in quality that affect low income groups".
This is because providers in most disadvantaged areas unlikely to be able to command the kind of high nursery fees that are charged in more affluent areas, it says.
As a result, it argues, children from low income families are more likely to be cared for by providers who are looking after more children per member of staff.
Chief executive Anand Shukla said: "The proposed changes to ratios will foster a two-tier quality system because parents can only choose the best childcare they can afford.
"We know from our focus groups that parents want generous ratios. Parents on higher incomes will demand that providers stick with generous ratios, but parents on low incomes won't have that choice.
"The result will be that children from low income families will be more likely to receive childcare from providers with the highest ratios and get less attention and support from staff."
He added that there was a vicious circle where parents, particularly those on low incomes, found that working did not make financial sense because of the high cost of childcare.
The charity's analysis of childcare costs suggests they are continuing to rise across the board. Next week it is set to give further details of how prices have risen across the board.
The warning comes after the Pre-School Learning Alliance condemned the planned changes at a conference on childcare.
Its chief executive Neil Leitch said: "Never in the past 12 years have I seen so much hostility towards a single initiative as this one. Why? Because we believe it entirely conflicts with the aim of putting the child first."
He said a recent survey for his organisation had found that 94% of group day care providers thought the quality of their childcare would diminish if ratios were altered.
"Yet, you would think that given around 70% of costs relate to staff wages, providers would be rushing out of their nursery doors jumping for joy at the prospect of increasing revenue - but it's the reverse."
The Department for Education stressed that the more flexible ratios would only be possible where there were highly qualified staff.
A spokesman said: "We are reforming the childcare system so that providers have more flexibility when they have highly qualified staff and childminders are better supported.
"Ratio changes, which are not compulsory, will allow providers to have the flexibility to increase pay for better qualified workers.
"High quality providers will be able to expand and more childminders will enter the market - this will mean parents have more affordable childcare.
"Ofsted will be the only arbiter of quality, removing any council duplication. As a result more taxpayers' money will go to the frontline.
"We want to help working families with costs and accessibility, and will make an announcement soon."
Plans in England to increase the child to nursery worker ratio could lead to a two-tier system, with a drop in quality in poor areas, a charity warns.