Mr Morgan issued the statement following a meeting with the regional secretaries of the four trade unions representing staff working in the merging bodies.
Mr Morgan said: 'Ministers are acutely conscious that organisational change on this scale inevitably means uncertainty for staff. Our aim is to tackle the transition as sensitively as possible and to ensure that staff are treated fairly and consistently throughout the merger process.
'The merger programme is not a cuts-driven exercise. The priority is to improve the way services are delivered to the public.'
The first minister gave his commitment that every effort is being made to secure jobs for those that want them within the Assembly civil service and indeed the wider public sector.
'I gave a commitment in a joint statement with the unions immediately following the merger announcement that the Welsh Assembly Government's 'partnership agreement' would apply to every aspect of the merger process.
'Through this agreement, all staff are fully consulted on proposals in advance of decision-making and staff representatives are involved in the drawing up of proposals in the first place. I am pleased that this is working well under the guidance of the Joint Negotiating Forum.
'I hope this clear message allays fears and underlines the way in which the mergers are being implemented for the benefit of our customers, businesses in Wales, training providers, and our staff.'