BBC director-general Tony Hall says in future the debate about the BBC's scale and funding "should be taken out of the political cycle".
His comments come as Culture Secretary John Whittingdale has appointed an expert panel to oversee a root and branch review of the BBC as part of the process for renewing the broadcaster's royal charter.
The broadcaster has agreed to take over responsibility for funding TV licences for over-75s from the Government as part of a deal agreed in the run-up to last week's budget.
Writing in The Observer, Lord Hall said: "As the dust settles after a challenging week of negotiation over funding and debate about the future of the BBC, three things are clear.
"First, the BBC has negotiated a strong financial settlement from the Government that gives us stability and clarity, but we should be in no doubt that the charter process will be tough.
"Second, despite noises to the contrary, the BBC is as independent today as it has ever been. There has been no fundamental change in the relationship between government and corporation. Nor will there be under my watch.
"Third, although the BBC used the pre-budget window of opportunity to reach a fair deal, it is not a process we would have chosen and it is not a process that should be repeated."
He said major efficiency savings will have to be found and difficult decisions taken, adding: "Successive governments have used the licence fee in different ways to fund priorities that are only indirectly connected to BBC output, for example, to support broadband rollout.
"So this is not a new debate and last week did not mark some seismic shift in the relationship between the BBC and the Government. Our independence is precious and will never be negotiated away.
"However, for people to have confidence in the country's most important news organisation, they must know that its journalists will ask the difficult questions without fear or favour.
"So I believe that in future the debate about the BBC's scale and funding should be taken out of the political cycle."
Meanwhile, the appointed advisory group includes former Channel 5 boss Dawn Airey, who has previously called for the licence fee to be cut and for the broadcaster to consider charging for its website, and former Ofcom chairwoman Colette Bowe.
The Sunday Times reported that a Government green paper due to be published this week will ask fundamental questions about the BBC's role, including whether it should stop chasing viewers and provide more public service programmes.
The presence of Ms Bowe on the advisory panel will fuel speculation that the green paper will propose that Ofcom could take over the role of the BBC Trust in overseeing the corporation, although the option of a new regulator is still on the table.
Other members of the panel include: Shazam executive chairman Andrew Fisher, Arts Council England boss Darren Henley, Johnston Press chief executive Ashley Highfield, former Shine Group chief executive Alex Mahon, digital entrepreneur Lopa Patel and journalism professor Stewart Purvis - a former editor-in-chief of ITN.
The Department for Culture, Media and Sport (DCMS) said the panel will provide strategic independent oversight and challenge to the charter review programme and bring to bear their own personal experience and expertise on the policy debates.
Mr Whittingdale said: "Each member of the independent advisory group brings individual skills, experience and expertise.
"Together they will contribute to the oversight of the Government's review of the BBC royal charter. I look forward to working with them on this important issue."
The green paper is reported to open the door to a replacement for the £145.50 licence fee, with various funding models including a household tax or subscription system being considered.
It will also suggest that the BBC website should be scaled back, question whether the corporation's news fulfils its obligation to be impartial, examine whether more of the broadcaster's output should be independently produced and consider the future of BBC Worldwide, the Sunday Times reported.
A DCMS source told the Press Association that "nothing has been decided yet" and "everything is still on the table".