The Environmental Investigation Agency (EIA) claims luxury apartments at the 47-storey Manchester tower - where Ian Simpson owns a penthouse - feature dark red merbau taken from Pacific island New Guinea's tropical forests.
Birmingham's Beetham Tower is also fitted with rare merbau wood, according to the independent environmental organisation.
Lancashire-based flooring manufacturer Atkinson & Kirby has been named by EIA investigators as supplying the wood on the £155 million Manchester Beetham Tower.
The EIA said Atkinson & Kirby supplied flooring for all 219 apartments - many of which are now owned by celebrities including England international footballers - but has not specified what percentage was endangered merbau timber.
The EIA said the firm is now sourcing Forest Stewardship Council timber to replace the merbau.
The agency has deliberately exposed the Beetham Towers as part of a campaign to bring in new laws banning the sale of illegal timber in the UK, where it is currently not a crime to import, market, distribute and sell timber from endangered trees.
EIA is now urging the Beetham Organisation to ensure timber in its proposed Liverpool and London towers can be 'proven beyond doubt' to come from legal origins.
Neither Ian Simpson Architects nor the Beetham Organisation were available for comment.
In a separate development, teams of so-called 'spidermen abseilers', normally employed to clean windows at the 170m-tall Manchester Beetham Tower, are being brought back to solve the building's noisy 'whistle' once and for all.
Engineers are blaming a thin glass blade on top of the structure, which vibrates in strong winds, for the noise, and will install a 'permanent solution' over the next five weeks.
The problem was identified after city-centre residents complained about an annoying hum coming from the building. Even nearby filming of soap Coronation Street had to be halted because of the whistle.