Hannigan, who has been in the post for more than three years, is to switch to the political directorate.
The move comes as a fresh round of talks start over re-establishing the devolved government in Northern Ireland, involving Tony Blair, Irish PM Bertie Ahern, Northern Ireland secretary Paul Murphy and the leading political parties.
The office aims to have a replacement for Hannigan in place by the autumn.
The role, which commands a salary of around £80,000, is responsible for setting the strategic direction of the Government’s communications work in Northern Ireland.
Hannigan’s successor will oversee a team of 30, including a deputy director, and will work closely with Murphy and 10 Downing Street.