The charge is in a complaint about the chairman of the Big Lottery Fund from shadow culture secretary Jeremy Hunt and shadow charities minister Greg Clark (Third Sector Online, 8 February).
The letter to Cabinet Secretary Sir Gus O'Donnell, head of the civil service, concerns Booth's remarks that the Tories were "hostile to the voluntary sector" and Hunt needed "a seminar in elementary arithmetic" (Third Sector, 30 January).
Booth is bound by Cabinet Office guidance that says members of non-departmental public bodies should not "make political speeches or engage in other political activities" in relation to their work.
The letter said Booth's comments were "wholly inappropriate for a public servant who is supposed to be politically neutral, in particular the personal nature of his attack on a member of the shadow cabinet".
There were, it said, "serious constitutional implications if a supposedly neutral figure is prepared to enter the political fray in this way".
A spokesman for the Cabinet Office said the letter had been received and it would respond. Booth declined to comment.