John Chamberlain, director of fundraising and communications at John Grooms, said job cuts would be a last resort.
He said: "We have large numbers of vacancies and people on temporary contracts. Our intention is to keep as many of our permanent staff as possible."
The future of Michael Shaw, chief executive of John Grooms, is also unclear after Mary Bishop, chief executive of Shaftesbury, was chosen to run the new organisation, Grooms-Shaftesbury. Chamberlain said Shaw's role had "yet to be discussed", but added: "We are very open to his involvement."
The merged charity is expected to be formally constituted early in the next financial year.