In a letter to PCT chief executives last week, Dr Colin-Thome said 'successful' referral management schemes would need to be developed in the 'context of broader health reforms'.
'First and foremost the vision and function of a referral management scheme must be developed and agreed with practice-based commissioners,' he warned.
The schemes have been set up by some PCTs to ensure patients are placed in the right setting for treatment following a GP referral, and not automatically referred to an acute hospital.
But foundation trusts have claimed some have been used to move patients away from the acute sector to underused independent sector treatment centres, and GPs say the schemes have removed their autonomy.
In the letter Dr Colin-Thome warns referral management schemes should not prevent practice-based commissioners from developing alternatives, and that many practice-based commissioning initiatives could 'reduce the need for the schemes by decreasing reliance on secondary care services'.
Last month the British Medical Association published a list of principles, endorsed by the Department of Health, outlining how referral management schemes and capture, treat, assess and support services run by PCTs should operate.
Speaking at the time of their publication BMA consultants and specialists committee chair Dr Jonathan Fielden said several referral management centre schemes had been a 'mess'.