In what is thought to be one of the first cases of its kind, the Christ Apostolic Church Mount Zion International in Peckham appealed to the government's Valuation Office Agency (VOA) over the London Borough of Southwark's request for it to pay £15,575 under the Community Infrastructure Levy (CIL).
The council collects the CIL on behalf of the London mayor, who is using a capital-wide charge on all new developments to help pay for the Crossrail project.
The church was granted planning permission in August to continue as a place of worship, after a temporary permission lapsed last November. It was handed the CIL liability notice at the same time.
Backed by the Greater London Authority, the council said because the premises have not been in continuous lawful use for six out of the 12 months before permission was granted, the church was liable to pay CIL.
But VOA district valuer Martin Single last week ruled that the church is exempt because it is a minor development under CIL regulation 42. In his report, he stated that regulation 42 applied because "there has been no new build greater than 100 square metres" and the development "does not comprise any dwellings".
Matthew Druce, of planning consultancy West & Partners, the church's agents, said he hoped those involved in applying the levy "will take note of the decision".
A council spokeswoman said the valuer's decision "was contrary to the council's view, which was strongly supported by the GLA", adding: "However, the appeal decision provides clarity on such matters should they arise in future."