Based in Downing Street and the Cabinet Office, Aiken will be the most senior comms professional in the civil service.
He will oversee the comms around the civil service reform programme and newly developed comms frameworks set up to replace the COI.
He is replacing Godric Smith, who has been in the role on an interim basis since the departure of Jenny Grey in the autumn.
The news comes shortly after PRWeek revealed that Smith was set to launch his own agency alongside London 2012 marketing director Greg Nugent.
Minister for the Cabinet Office Francis Maude said: 'I would like to thank Godric for the work he has done over the past few months and I hope he considers returning to Whitehall at some point in the future.
'I am pleased to welcome the appointment of Alex Aiken as executive director of government communications. He will help drive forward the communication of our civil service reform programme and our plans to save the taxpayer money by establishing shared communication hubs for government.
'Alex brings with him tremendous expertise and experience. He has a strong track record of delivering communications that represent value for taxpayers’ money.'
Aiken said: 'I am delighted to be taking on this role and will focus on delivering effective and efficient government communications. The civil service has excellent communications staff at every level and I look forward to leading the whole profession in delivering the highest standards in explaining government policy.'