On Wednesday in Paris, FOTA chairman Luca di Montezemolo sat with the FIA president as well as Bernie Ecclestone as they announced an agreement had been reached to move on after weeks and months of bitter feuding.
But Mosley interpreted the subsequent media coverage of the agreement as manipulated by Montezemolo and the eight rebel teams, keen to portray the deal as a successful coup that had resulted in victory as well as his head.
The 69-year-old wrote a letter to Ferrari's Montezemolo demanding a retraction and apology, but on Thursday the Italian instead issued a backhanded compliment by thanking Mosley "for his decision to leave the FIA in October".
Mosley, now openly rethinking his retirement, is reportedly also furious at FOTA vice-chairman John Howett's appeal to the World Motor Sport Council that it elect an "independent" president to succeed the incumbent.
He has now written another letter to the FIA member clubs, in which Mosley alludes to Howett's comments that "concern me greatly" and to Montezemolo who "did not keep his part of the bargain".
"We must continue to defend the independence of the FIA, even if this leads to difficulties in the sport," Mosley wrote.
He said the aftermath of the agreement had become "intolerable" and warns that, despite this week's declaration of peace, formula one now faces another "difficult period".
"This may well result in short-term problems in formula one," added Mosley. "It is possible FOTA will set up an independent series. The championship has had difficult times in the past, and no doubt will again in the future."
He accuses FOTA as being a body with "no sporting ethics" and "under the control" of the car manufacturing industry "we have constantly to monitor".
Even more provocatively, Mosley revealed that one manufacturer team lobbied him to ignore the processes of the Court of Appeal and simply declare 'double diffusers' illegal earlier this year.
He also said that when the FIA championed the road car safety standards system Euro NCAP, "one of the major manufacturers threatened to quit formula one" in protest.