Waitrose said the move was a statutory six-year review and not linked to Brand Connection's merger. However, there could be a potential client conflict, as Initiative has Tesco as a client.
Brand Connection had been hit by the loss of the £64m Norwich Union account to OMD UK last December as part of the consolidation of the £75m Aviva brief. Brand Connection had held the Norwich Union business for 21 years.
The agency's managing director, Richard Britton, deputy managing director and planning director Sarah Jennings, and client services director Simon Timlett are all believed to be staying on within the Interpublic Group.
Both Britton and Jerry Hill, co-COO of Initiative EMEA, refused to comment on the merger.
Another Brand Connection client is Body Shop, which was acquired by ZenithOptimedia client L'Oreal for £652.3m earlier this month. Also, the £7.5m planning account for HP Sauces moved to Vizeum in January, along with the Carat-based buying business.
Brand Connection has approximately 50 employees and more than 40 clients including Metro Goldwyn Mayer, William Hill bookmakers and Del Monte.
The agency is split into eight core teams including management, client service, business planning and research, television trading, non-television trading, direct response, digital interactive media and recruitment.
The move will also mean that ID Media, the direct arm, a joint venture between Brand Connection and Initiative, will be folded into Initiative.