The resignation of a second member of the clergy at St Paul’s Cathedral cast a shadow over its reopening yesterday.

The cathedral opened its doors again on Friday with a special lunchtime service two weeks after being closed for the first time since World War II because of anti-capitalist protests.

The reopening came amid fierce criticism towards the cathedral for its handling of the Occupy London Stock Exchange demo outside its doorstep.

The resignation of cathedral chaplain Fraser Dyer comes just days after Canon Chancellor of St Paul’s, the Rev Dr Giles Fraser, stepped down in protest against the forced removal of protesters camped in the churchyard.

Rev Dyer, who also serves as curate at St Peter De Beauvoir Town in east London, said in a statement that he was embarrassed by the cathedral’s position on the protest.

He said: “I do not relish the prospect of having to defend the cathedral’s position in the face of the inevitable questions that visitors to St Paul’s will pose in the coming weeks and months, particularly if we are to see protesters forcibly removed by police at the Dean and Chapter’s behest."

He added: “I am sorry that the story has become one about the Church and not about the City.”

Cathedral Dean the Rt Rev Graeme Knowles confirmed on Friday that legal action has “regrettably become necessary” after several requests to leave voluntarily were turned down by protesters.

“The Chapter only takes this step with the greatest reluctance and remains committed to a peaceful solution,” he said in a statement.

“At each step of the legal process the Chapter will continue to entreat the protesters to agree to a peaceful solution and, if an injunction is granted, will then be able to discuss with the protesters how to reach this solution.”

Anglicans remain divided over how to deal with the demonstration that sprang up when Occupy Wall Street went global.

The Bishop of London, Dr Richard Chartres, said he supported the position of cathedral officials in removing protesters. The Bishop of Buckingham, Alan Wilson, said the decision to close the cathedral’s doors had been a “hysterical overreaction”.

Several Christian organisations have expressed their solidarity with the protesters, including the Student Christian Movement and the Fellowship of Reconciliation.

In a joint statement, they said: “As Christians, we stand alongside people of all religions and none who are resisting economic injustice with active nonviolence.”