The Christ Apostolic Church Mount Zion International in Peckham has objected to the London Borough of Southwark's request for it to pay £15,575 under the Community Infrastructure Levy (CIL).
Southwark Council collects the CIL on behalf of the London mayor, who is using a capital-wide charge on all new development 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.
The council, backed by the Greater London Authority, argued that, because the premises have not been in continuous lawful use for six out of the 12 months before permission was granted, the church is liable to pay CIL.
But the church's agents, planning consultancy West & Partners, have appealed to the government's Valuation Office Agency (VOA).
They argue that CIL regulation 40, on which the council's argument is based, does not stipulate that the premises must have been in a "lawful" use for six continuous months.
They also argue that the church should be exempt because it is a registered charity, after applying for charitable relief in July.
The council rejected the relief application because, it said, it had been made before permission was granted and was therefore invalid.
A council spokeswoman said: "We advised the church that they should apply for charitable relief before they started any use, but they did not. Unfortunately, this means we have been required to seek the payment."
West & Partners have also pointed out that the planning application was submitted last October, while the church was in lawful use, and it took nine months for the local authority to reach a decision.
A VOA spokeswoman said the agency has so far decided just one CIL appeal since the provisions came into force in 2010, but refused to comment further.