The Church of England's second-most senior cleric, Stephen Cottrell, will call in a Christmas sermon on Wednesday for repentance and change within an institution reeling from child abuse cover-up scandals.

This year's festivities have been overshadowed by the Archbishop of Canterbury Justin Welby's resignation over a cover-up and accusations of further safeguarding failures by his number two Cottrell, who is the Archbishop of York.

In addition to its 16,000 churches in England, the Church, which traces its roots to the Roman Empire, is also the mother church for 85 million Anglicans in over 165 countries.

"Right now, this Christmas, God's Church itself needs to come to the manger and strip off her finery and kneel in penitence and adoration. And be changed," Cottrell will say at York Minster in northern England, according to extracts shared by his office.

Welby, who stepped down in November following a report that he had failed to take sufficient action to stop prolific sex abuser John Smyth, will not deliver the main Christmas sermon at the historic Canterbury Cathedral.

"At the centre of the Christmas story is a vulnerable child; a vulnerable child that (King) Herod’s furious wrath will try and destroy, for like every tyrant he cannot abide a rival," Cottrell will say.

"The Church of England – the Church of England I love and serve – needs to look at this vulnerable child, at this emptying out of power to demonstrate the power of love, for in this vulnerable child we see God."

Welby is due to complete his official duties by Jan. 6, with the process to pick his successor expected to take up to six months.

Cottrell, who will effectively run the Church until then, has also faced calls to resign following a BBC report that he let priest David Tudor keep his job despite knowing the Church had barred him from being alone with children and that he had paid compensation to a sexual abuse victim.

Cottrell has apologised for not having been able to act sooner when he was the bishop of Chelmsford, saying the situation he had inherited was "horrible and intolerable" and that he suspended Tudor at the first opportunity.

The British public, increasingly less religious and church-going, has been bitterly critical.

David Greenwood, a lawyer specialising in abuse claims, said in a statement the revelations had "shaken trust in the Church's ability to protect its congregants and uphold its duty of care".