The NML accuses the chairman and the board of trustees of FNML of being "unsupportive" of the work of NML and pursuing its own agendas.
The FNML, for its part, criticises NML for "dumbing down" its exhibitions and museums.
And, certainly, the abrupt dismissal of FNML - which has given more than pounds 800,000 in grants to NML to purchase artefacts and items, on top of hundreds of thousands of hours in unpaid volunteer time over the years - smacks of paranoia and a lack of confidence at the top of this important institution.
Last night, FNML chairman Andrew Pearce said he was angry and disappointed that, just because the group took different views to those of the NML, it had to be done away with.
NML's director of communications, Amy de Joia, said that, for a considerable time, the chairman and the board of trustees of FNML had been "unsupportive" of the work of NML and pursued its own agendas.
A new membership scheme, no longer linked with FNML, has been set up by NML.
FNML was formed in 2003 from the Friends of the Merseyside Maritime Museum and Friends of National Museums and Galleries on Merseyside, following the merger of the respective institutions into NML.
In January, NML director Dr David Fleming wrote to Mr Pearce to express "disappointment" that FNML had failed to give a grant for the International Slavery Museum, which had been requested.
Ms de Joia states the "overt lack of support from FNML has, in our opinion, been inexcusable".
it is clear to us that there has now been a fundamental breakdown in the relationship between NML and the FNML committee."
In a statement released last night, Ms de Joia added: "In the interests of the museum service and the wider public, NML has set up a new membership scheme that will no longer be linked to FNML.