BBC News website editor Steve Herrmann said the new-look site will not revert to its previous design, despite complaints of it being "fussy" and "chaotic".
Thousands of people have responded to Mr Herrmann's updates on the BBC's Editors blog explaining the revamped site - and he acknowledged most comments have been "critical".
But the BBC boss said going back to the old design was not something that was being considered.
The BBC billed the new design as being "clean" with "more space for the main stories of the day", with better navigation and making it easier to see which stories are the most recent.
But members of the public have been airing their grievances online, with one commenting on the Editors blog: "My eyes are distracted by the fussy layout, everything tightly crammed together ...
"Everything has a squashed feel and is something I would expect from a child."
Mr Herrmann wrote on his BBC blog: "Thank you for all your feedback on the BBC News website redesign.
"There has been a lot of it, and we'll continue to sort through the comments and emails we've been receiving, identifying specific issues we can address and adding answers to the Frequently Asked Questions (FAQs) page.
"Most of you commenting here on the Editors blog have been critical, with many urging us to change the design back to the way it was.
"Given the strength of feeling expressed in some of the comments, I'd like to explain again, as clearly as I can, what our thinking is."
He said going back to the old design "is not something we're considering, but building and continuing to improve on the changes we've made certainly is".
Mr Herrmann said the BBC was looking closely at feedback on the new design and if changes needed to be made, they would be considered as part of a review process.
He said the changes were based on "careful research" but added: "There are a few things not yet working exactly the way they should be - our developers and designers are tackling those now".
Another internet user said they felt insulted and wrote: "We have all read the FAQs and the numerous blogs from yourself and others on this matter ...
"This doesn't change the fact that so far the vocal majority do not like the changes."
Another web user wrote: "Why don't you just stop thinking and put it back the way it was?
"You have just acknowledged that most of us are unhappy with what you have done, yet you persist with this debacle."
Another user declared: "Horrible, horrible, horrible new layout. Difficult to use, difficult to find things you want."
Someone else wrote: "Don't like it ... if it ain't broke don't fix it," while another web user described the site as "needlessly chaotic and glitzy".
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