At a meeting of the Full Council, Tower Hamlets Labour Group successfully proposed a motion calling on the Council to support the More Light More Power campaign.
Mayor of Tower Hamlets John Biggs also attended a public event in November to speak against the plans, alongside Hackney Mayor Jules Pipe.
The Mayor of London called in the £800m scheme last year.
At a meeting of the Tower Hamlets Strategic Development Committee in December, members agreed that if it was empowered to decide, the Council would have refused permission.
Mayor John Biggs said: “It’s important that we continue to make a strong case against the Goodsyard scheme. The full implications of the proposals have to be considered, not just waved through by the Mayor of London.
“It is very worrying that Boris Johnson seems to have disregarded the right of both Tower Hamlets and Hackney to a local planning process, instead choosing to make the decision by himself. I would urge residents to respond directly to the public consultation, which is open until February 15th.”
Councillor John Pierce commented: “The scale of the proposed Goodsyard development is massive and residents were very disappointed that the Mayor of London saw fit to call the decision in, rather than allow the local authorities to make the final decision.
“The proposed level of affordable housing is simply unacceptable and is nowhere near our targets. With the housing crisis as serious as it is, the last thing we need is a potentially damaging development with a negligible amount of affordable housing.
“We have strong concerns that the environmental impacts of this development will be really damaging. There will be a serious impact on the right to light and air quality.
“In agreeing the motion, Tower Hamlets Council has sent a strong signal to Boris Johnson that he should listen to residents’ and the Council, rather than ignore the very real concerns about the development.”