The Radio Times has accused the Department for Culture, Media & Sport (DCMS) of not taking its readers' views on the future of the BBC into consideration.
A BBC Royal Charter Renewal Public Consultation on Culture Secretary John Whittingdale's plans for a reform of the corporation was launched in July 2015.
The Radio Times published 16 questions which, it said, mirrored those in the DCMS's official consultation.
But in a letter dated 11 March, the magazine said at least 6,000 digital responses delivered to the DCMS on an encrypted memory stick for data protection purposes were not included.
The Radio Times said the DCMS published its consultation report without requesting the password to open the file, "and therefore cannot have taken the responses into consideration".
The publication said Mr Whittingdale had told the Oxford Media Convention on 2 March that "every response has been read".
In a statement, a DCMS spokesman said the Government is "committed" to a "thorough and open" BBC Charter Review process.
"All responses to our formal consultation will feed into the process," the statement said.
"We also received other views including results from the Radio Times survey, which asked different questions.
"We will also take account of these as part of the Charter Review."
Radio Times editor Ben Preston said he finds it "absolutely baffling" that the contribution of 9,000 Radio Times readers, with 3,000 responses sent by post, were not considered.
In a statement, he said: "It is only thanks to an encrypted memory stick that we discover his department has not taken into consideration the wise words of so many people who have a genuine passion for quality broadcasting, despite claiming every response has been read".
He added: "The future of British broadcasting is too important to be carved up by politicians alone and the Secretary of State should reopen the consultation and listen to all the voices of the British viewing public."
In one of the largest ever responses to a government public consultation, in total 192,564 responses were received via emails, letters and an online survey.
The results were published on 1 March.
The consultation revealed the majority of respondents backed the BBC and its independence from government.