Sajid Javid said "everything" would be looked at, including licence fees and governance structures, when negotiations get under way.
Senior Tories have previously called the compulsory annual charge made to viewers out of date and warned it faces the axe but BBC executives insist a subscription system could end up costing more money.
Mr Javid said plans for renewing the charter, which expires in December 2016, were being worked on.
He said: "We will announce plans in due course. That will be a time to look at all aspects of the BBC: governance arrangements, licence fees and so forth. That's where we plan to look at everything."
The renewal negotiations will take place on the back of a torrid few years that have seen the corporation lambasted for its handling of the Jimmy Savile scandal, massive executive pay-offs and a Newsnight investigation that led to the late Lord McAlpine being wrongly accused of child abuse.
Tory John Whittingdale, chairman of the Culture, Media and Sport Committee, reportedly told senior BBC executives earlier this month that he did not believe the licence fee would survive.
The Government has frozen the fee at £145.50 for the rest of the charter period.