Speaking in the House of Lords, Bishop John Packer warned that the system was at risk of becoming more complicated just as it is becoming more crucial to parents.
"There is such a complex system, which is part universal and part not, with childcare vouchers in their varied forms as an additional complication," he said.
"Rather strangely, there is also the danger that universal credit will actually make the situation more, rather than less, complex.
"There is indeed a very strong case for extending access to affordable childcare, but there is also a case for starting again to provide a coherent system."
He proposed the establishment of an all-party commission to consider the possibility of a "more coherent" long-term strategy for childcare.
Such a strategy, he suggested, should take into consideration provision that is affordable as well as high quality.
"That we have here a system that is at the same time expensive and low-wage needs looking at carefully," he said.
He warned that low pay was linked to a high turnover in childcare staff, something which he said "needs to be combated".
"This must have an effect on quality. I know from my own experience how much my own grandchildren value the particular relationships that they establish through the childcare that is provided for them, and how difficult it can be for them and their friends when there are changes in that childcare," he said.
Bishop Packer went on to raise concerns about childcare provision in poorest families, especially those in work.
He warned that the cost of childcare was taking an increasing proportion of families' income, noting that more than half the families living in poverty are in work.
He also expressed concern for lone mothers and the unemployed seeking to get back into work.
"We need to ensure that the main beneficiary of childcare is the child," he said.
"Children in poverty need the high-quality childcare that enables their parents to work and so contributes to the well-being of the whole family."
In her response, Baroness Northover said the Government was improving support for middle-income families with the introduction of a new tax-free childcare scheme, while for low earners, the Government will continue to pay up to 70 per cent of childcare costs through working tax credit and universal credit.
She added that the Government was in the process of considering responses to a recent consultation on tax-free childcare and would respond shortly.