England's 152 PCTs are merging into around 50 clusters to save resources as PCTs begin to hand over commissioning responsibility to consortia.
Dr John Galuszka, from Oxfordshire's GP consortium, said the announcement that his PCT must join a cluster had been 'disappointing' and could end important relationships between emerging consortia and managers.
'Out relationship with our PCT is good and we were getting on well. As part of the transition we were hoping to have a bit of time to look at the people and functions that were most important and having a smooth transition. The clustering has to be destabilising for our people in the PCT - for us it is a negative thing.'
Surrey GP pathfinder consortium member Dr Charles Alessi wrote to the chief executive of London's south west cluster this month in a bid to avert any potential problems.
'We have concerns that centralisation and a focus on the cluster may hinder the development of the Kingston GP pathfinder,' he wrote.
'Recent attempts to limit the ability of pathfinders to influence commissioning and contracting are not welcome or supported,' the letter adds.
'We look to the south west London chief executive to give the pathfinders support in the development of these services.'
Dr Alessi was keen to stress however that there was no conflict with the cluster, and that the pathfinder was making 'great strides' in influencing commissioning.
Dr David Jenner, GMS/PMS lead at the NHS Alliance, said in his area the clustering had been dealt with fairly and he felt it was necessary.
'I can imagine it would be different in each locality but that depends on whether you get the people you want.'
Dr Jenner predicts that there will eventually be around 50 regional outposts of the new NHS Commissioning Board as remnants of the current PCT clusters.