Hello and welcome to the site. Thank you for your question.Building an extension to an existing building would only qualify for zero-rated VAT if all the conditions stipulated in Para 3.2.5 of VAT Notice 708 are met. Here is a link to the said VAT Notice
I am sorry if this is not the answer you were expecting.
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I was well aware of the VAT notice and I had really expected you to address the question specifically viz the church is a charity and seeking to provide an office for a disabled minister.
Thank you for your reply.There used to be a concession for approved alterations to listed buildings but this was changed in 2012.There are grants available towards VAT paid on repairs and maintenace to listed places of worship but in my opinion it does not cover extensions to be built to meet the needs for an office for a disabled minister.More information on the grants can be found here
Here is a link to a briefing paper from the House of Commons Library on this subject
I hope this is helpful.