Affordable housing residents in a new enclave of 3,400 homes are being prevented from using a luxury swimming pool and gymnasium, which are being kept for the exclusive use of private owners and renters.

Residents paying taxpayer-subsidised rents at Royal Wharf in the London borough of Newham have complained they are victims of segregation because they will not have access to a state-of-the-art clubhouse that neighbours who own or rent privately will enjoy.

Homes in the complex on the north bank of the Thames sell for up to £1.2m but 243 apartments have been made available to people on lower incomes at 60% of market rent as part of a flagship scheme by the London mayor, Sadiq Khan, to try to fix the capital’s housing crisis.

Up to about 500 residents are affected and some have branded the decision unfair because it appeared to discriminate against them because they were less well-off than the other people at the estate.

Residents who live at Royal Wharf under the mayor’s London living rent arrangement qualify for homes only if they are already renting and have a household income of less than £60,000 a year. Priority is given to families with children and people who live or work in Newham, which has some of the highest levels of deprivation in the country. It is supported by a £6.7m subsidy.

Marketing materials for properties for sale on the estate had described the swimming and hydrotherapy pools, sauna, steam room and gym as “a perfect platform for bringing people together”. But the landlord, L&Q, a housing charity, has said its tenants will not have access to the facility and Ballymore, the developer, said they will not be able to buy individual memberships.

Ade Eros, 37, a father of two who moved into a three-bedroom flat this summer, said it was wrong. “We don’t know why we are being segregated,” he said. “Whatever the reason for the policy, it is not fair. They should be motivated to include everyone.”

He said it was “sad because we were looking forward to using it with my two boys and them learning to swim”.

Another resident, who asked not to be named, said it was “like social cleansing”.

“We’re the poor relations,” she said. “It’s really unfair.”

Another complained that he was having to use a gym a couple of miles away in Canary Wharf.

Leaseholders, on the other hand, will get access to the clubhouse as part of their service charge. It opens in December and has a “technogym” staffed by personal trainers running courses in Zumba, yoga and pilates. Tenants of private flats will have to pay only about £45 to join.

The deputy mayor of London, James Murray, said: “It would be plain wrong if residents in the London living rent homes were not able to access memberships to the leisure facilities when they open. We will contact Ballymore’s senior management to make clear our expectation that these facilities must be available to all residents.”

The arrangement emerged after widespread concern at social housing residents being forced to use side doors to apartment blocks that also contain private flats, a phenomenon being dubbed “poor doors”.

Planning policy has encouraged affordable and private housing to be blended so that they look similar, but city flat dwellers have found that even bicycle storage spaces, rubbish disposal facilities and postal deliveries are being separated.

A spokeswoman for L&Q said: “It is policy not to pay for universal access to extras such as a clubhouse as not everyone would use this amenity and it does not provide value for money. Royal Wharf is no exception and we marketed the properties on the basis that access to the clubhouse was not included.”

Up to 17% of the homes in the development are classed as affordable, well below the London target of 35%, although Ballymore said it was making cash contributions to affordable housing elsewhere in the borough.