Zai Bennett, who took over as controller of the digital channel in 2011, said it had won "numerous" awards "on a fraction of the budget of the big boys".
He said: "I find it slightly perverse that I am writing about the fact the station will cease to be a linear channel from next autumn."
The decision to move the channel was announced last week and is expected to save £50 million a year.
Mr Bennett said it was "an enormous risk".
He said: "I and the small but dedicated BBC3 team were all shocked, but it is heartening that after the news sank in everyone talked about not only how to make this change work, but how to ensure the new BBC3 is world class.
"I am confident that the strength and depth of the existing brand, its talent, its suppliers, its staff and the love of its audience give it more than a fighting chance."
About 187,000 people had signed an online petition opposing the move, less than a week after the decision was made public.
BBC funding is in the spotlight with its charter up for renewal in 2017.
An internal report into the subject recommended increasing the licence fee in line with inflation and raising the amount of money the BBC makes through commercial ventures.