The decision appears to signal a death knell for the internationally acclaimed architect's relationship with the institute and represents another missed opportunity for him to build a significant public project in Britain.
The institute is currently in the process of recruiting a construction project manager to oversee a fresh feasibility study that will assess building a new film centre somewhere in London.
This move - which is likely to be announced formally next week - has the backing of Ken Livingstone's London Development Agency (LDA).
Chipperfield had been working with the BFI since 2001, when he won a competition to design a new headquarters for the institute on a site next to the London Eye on the South Bank ( pictured).
His practice looked at several potential homes for the BFI, including the possibility of a site adjacent to Tate Modern on Bankside, before the institute's bosses fell 'suspiciously quiet' 12 months ago.
Chipperfield was also cold-shouldered last year when Keppie took over the lead on his BBC Scotland headquarters in Glasgow.
Chipperfield said he was 'particularly disappointed' that the BFI failed to inform him that it had decided to start again with a new team.
'We met them [the BFI bosses] 12 months ago and they insisted there was no way we were being replaced,' he told the AJ. 'But then they went quiet and we heard that John McAslan was advising them.
'We had done a lot of work for them. If they wanted to keep us on they certainly could, but they [the BFI] seem to want a new team.
'That is very frustrating. A fresh competition for an architect will take a long time and money. A lot of people, such as Deyan Sudjic and Nick Serota, gave up time to be on the jury that picked us in the first competition.
'There are times when this kind of behaviour is permissible, but this is a very strange case,' he added.
The BFI was cagey about its intentions, but following repeated enquiries a spokesman admitted there are new plans in the pipeline.
'We have launched a feasibility study, with the support of the LDA, to look at building the cultural, social, economic and regeneration case for the BFI to create a new film centre in London,' he said.
The spokesman insisted that Chipperfield had not been dropped completely. 'We are in the process of appointing a lead consultant, although no decision has been made yet,
but we are certainly not engaging any architects at this stage,' he added.