The bishop of London has broken ranks with the City of London Corporation over planned legal action to evict the tented encampment outside St Paul's Cathedral in London.

Dr Richard Chartres is expected to urge the chapter of St Paul's – which has been hit in the past week by the resignation of two senior officials – to dissociate itself from the legal action to expel the protesters.

The move could strain relationships with the City of London, but is seen by the bishop as an attempt to rescue the Church of England from the damaging publicity surrounding its stance towards the Occupy London protest.

The protesters will be given an ultimatum on Tuesday: remove your tents in two days or face court action.

The City of London Corporation is expected to serve legal papers on them the day after it warned them to remove their tents from land it owns around the cathedral. The home secretary, Theresa May, gave the authorities her full support on Tuesday morning.

"The police and the church and the Corporation of London need to work together to clear the protest as soon as possible," she told ITV's Daybreak. "Obviously what we've heard today, I think, is that legal action is being taken."

The eviction moves follow the resignation of the cathedral's dean, the Right Rev Graeme Knowles. He became the third cleric to leave his post as a result of the Occupy London protest, after the canon chancellor of St Paul's, Giles Fraser, and the part-time chaplain Fraser Dyer.

The archbishop of Canterbury, Rowan Williams, made his first comment on the dispute on Monday, saying: "The events of the last couple of weeks have shown very clearly how decisions made in good faith by good people under unusual pressure can have utterly unforeseen and unwelcome consequences, and the clergy of St Paul's deserve our understanding in these circumstances."

Protesters had been expecting eviction warnings from the corporation on Monday but they were never served with any papers. St Paul's authorities have previously said they too would seek a high court injunction to remove the encampment from land in its ownership, but have taken no similar action.

Ian Chamberlain, 27, from Occupy the London Stock Exchange, said: "They have to serve that notice and give us 48 hours so there is room for us to respond with legal action or whatever.

"Our invitation for dialogue is still there. Liberty [the human rights group] offered to facilitate a meeting to have dialogue with the Corporation of London and they haven't responded yet. We will stay here right until the end and explore legal options to respond to any eviction notice we do receive."

At least 12 people were arrested at a separate demonstration outside the Houses of Parliament against plans to criminalise squatting.