The outcome will turn on whether the motorised platform, which Thames Heliport wants to float between Chelsea Bridge and the Thames Barrier, requires planning permission like a fixed structure on land.
To reduce the concentration of noise, it will move continually between the site's 22 piers and flights will land wherever it is moored.
The scheme is believed to be the first planned over water, and the Civil Aviation Authority is said to have agreed the plans on safety grounds.
Tower Hamlets is leading the other authorities in the challenge to determine whether the plans can be described as a development under the 1990 Town and Country Planning Act. The boroughs all wish to oppose the heliport, but cannot do so on environmental grounds alone because the project will not be on land.
'We are acting as a lead authority on behalf of the other nine boroughs affected by this proposal. Eleven of the 22 approved locations on the river border us,' said Tower Hamlets press officer Jean Hindry.
'This appears to be a grey area of the law with both sides having conflicting legal opinions.'
A date has not yet been set for the court hearing.
Residents who fear their houses lie under the proposed flightpaths are worried that they will suffer from aircraft noise over their homes and gardens.
Christine Shawcroft, a Tower Hamlets councillor, said many local people were opposed to this 'heliport hell'.
Helicopters create more noise on landing than on take-off. Among the models Thames Heliport hopes to use is the 12-seater Sikorsky S76, one of the loudest and heaviest light-to-medium size craft flying.
Thames Heliport wants to start services this year or early next. It says a maximum of 22,000 take-offs and landings will eventually take place each year - around 1,000 movements from each site.
But Johnny Moss, a director of the company and a former Army helicopter pilot, said he is determined to work with residents to ensure flights do not blight their neighbourhoods.
'We would like to enter a legal agreement with the boroughs over the flights. If we break the rules we will be penalised. We do care, and we are looking for a way to work with the boroughs.'
Flights will be scheduled from 7am to 11pm, with the majority between 8am and 5pm. Most will cater for business people, providing airport shuttles and hops to and from Paris, but around 30 per cent will be pleasure trips.
Mr Moss said the central London heliport was a necessity rather than a luxury. 'London needs helicopter facilities. Battersea heliport is in the wrong place, and businessmen are ready to use this site.'
The Westland London heli-port has occupied its site on the south bank between Wandsworth and Battersea bridges since 1959. It handles a maximum of 12,000 movements a year. Transfer times to the City can take up to 45 minutes.
'YES AND NO' PUZZLE OF PLANNING CONSENT
Planning rules are complex and some large developments do not need permission, while smaller ones do. An existing industrial building in an urban area can grow by 25 per cent without local authority permission.
Companies laying tramways are exempt from applying from express permission and can install overhead wires, tracks, underground cables, as long as their work is carried out on a road and does not exceed a 15m height limit.
Air traffic developments on land, such as heliports, runways or new terminals, are subject to standard planning regulations and can result in major public inquiries.
Three years ago a Redbridge woman who built a mud hut, using old doors and other scrap, in the back garden of her council flat was forced by the borough to apply for planning permission - which she won - solely because people living above her could look down on to her garden.
Had she lived in a house with neighbours on the same level, she would not have needed to apply for planning permission.
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