On the death of
Roger Ascham he was recommended to succeed him as Latin secretary to the queen by
Sir William Cecil,
Robert Dudley, 1st Earl of Leicester, and
Walter Haddon. The office, however, was granted by the Queen to
John Wolley. About the same time he was accused of unsoundness in religion, but defended himself. In 1569 he was again elected proctor of the university. On this occasion he was publicly charged with unsoundness in religion and reproached for having been rejected at court. The Earl of Leicester, in a letter to the vice-chancellor and regents of the university, dated 11 May 1569, vindicated Clerke's reputation. To the parliament which assembled on 2 April 1571 he was returned as one of the members for the borough of
Bramber in Sussex, and on the 19th of the month he took part in a debate on the bill against
usury, his speech containing quotations from Aristotle, Plato, St. Augustine, and the psalmist. In that year he accompanied to Paris
Lord Buckhurst, sent as ambassador to the French court to congratulate
Charles IX on his marriage. He resided with his lordship for some time after his return to England, and he was also held in esteem by
Edward de Vere, 17th Earl of Oxford, to whom he was a tutor at Cambridge University. He was also a correspondent of the Earl. It was in 1571 that
Nicholas Sanders printed his book,
De visibili Ecclesiae Monarchia.
Lord Burghley and Archbishop
Matthew Parker thought it ought to receive a substantial answer from a jurist, and Clerke was asked. Burghley desired some public testimony from the university respecting Clerke's conduct: the vice-chancellor and
John Whitgift as Master of Trinity College, testified on 6 December 1572 to his good reputation for learning. While engaged in refuting Sanders, Clerke was accommodated with a room in the Arches by favour of Archbishop Parker, who himself assisted in preparing the reply, which was then scrutinised and corrected by Burghley before it was sent to the press, as
Fidelis servi subdito infideli responsio. It was printed by
John Day, and trouble was taken with the typography, but Day asked Parker for a
quid pro quo in the shape of help with setting up a book shop. ==Ecclesiastical lawyer==