Concerns about plans to scrap NHS primary care trusts and strategic health authorities have been listened to, the government said.
Many GPs have already signed up to take over their local NHS budgets and will become responsible for planning hospital care and services for patients from 2013 under government proposals.
But unions, think tanks and health campaigners have voiced fears that reforms are being introduced too quick and could hinder patient care.
Unite said health secretary Andrew Lansley was driving the NHS into "the buffers" by moving too fast and without proper consultation.
The union, which has 100,000 members in the health service, said the plans were heading "in the wrong direction" and had been "cobbled together".
Later, the government will outline its priorities for the NHS in the coming year as part of the NHS operating framework.
Mr Lansley announced that part of it would include hospitals being "held to account" and fined if they fail to get rid of mixed sex wards.
In its response to the consultation on its white paper, the government said it had listened to concerns about the structural overhaul of the NHS.
It has made some amendments, including placing commissioning of maternity services with GPs instead of with a National Commissioning Board.
It has also pledged to "allow a longer and more phased transition period" for completing some of the reforms, such as keeping the regulator Monitor on board for some control of foundation trusts.
It has also promised to "create a clearer, more phased approach to the introduction of GP commissioning" through the pathfinder pilots.
"This will allow those groups of GP practices that are ready, to start exploring the issues and will enable learning to be spread more rapidly," it said.
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