A concert broadcast by the BBC from Methodist Central Hall Westminster has been criticised on social media for Williams' foul language and the skimpy apparel of his backing dancers, which some Methodists felt were inappropriate for a church building.
The building near London's Parliament Square is used as a conference centre as well as having a thriving congregation and has previously been criticised for hosting a UKIP party conference.
Superintendent minister Rev Martyn Atkins and the conference centre's managing director Paul Southern said they were "saddened and disappointed" by Williams' behaviour.
In a statement they said: "Central Hall Westminster Ltd agreed with and made clear to the BBC, as it does to all its many clients, the terms and basis for events taking place here, recognising it is – and remains – a place of Christian worship in the Methodist tradition.
"It is clear from the 'live on-air' comments by Robbie Williams that these had been communicated to him, ('I've been asked by 50 people at the BBC not to swear') but he chose to ignore this. We are saddened and disappointed that Robbie Williams chose to do this and are assured that Central Hall Westminster Ltd will be communicating our concerns and those raised by others to the BBC."
However, they added: "Despite this particular event, we remain delighted that this special place hosts so many fine, worthwhile and wonderful occasions.
"Public worship took place here on Sunday January 1, as on every Sunday, when a full chapel marked a new year and committed themselves to God and the purposes of God's kingdom."