A development consent order (DCO) application for the Riverside Energy Park was submitted to the Planning Inspectorate (PINS) by waste management firm Cory in November last year.
According to a statement from the mayor's office, Khan today sent a report to business secretary Greg Clark outlining his opposition to the plans.
At the same time, the London mayor called on the government to stop permitting "archaic" waste incinerators and said ministers should instead focus on boosting recycling rates.
Khan said modelling carried out by City Hall showed London has enough incineration capacity if the capital’s waste reduction and recycling targets are met.
He said: "London’s air is a toxic air health crisis and the last thing we need, in our modern green global city is another harmful waste-burning incinerator polluting our city."
In a representation on the DCO application, the Greater London Authority (GLA) said the project would be in conflict with the National Policy Statement for Energy, which states that only waste that cannot be recycled should be used for energy recovery.
The GLA also said the impact on air quality would be in conflict with the London Plan and there was "insufficient foreseeable heat demand in the local area" for such an energy from waste facility.
According to the GLA, there are already three incinerators in the capital - in Enfield, Lewisham and an existing facility on the application site in Bexley. The GLA said the new plant would emit more than four times as much nitrogen oxide as the existing incinerator.
Khan added: "Instead of granting permission for an unnecessary new incinerator that will raise pollution levels in the boroughs of Bexley and Havering, the government should focus on boosting recycling rates, reducing the scourge of plastic waste and tackling our lethal air. I am urging ministers to reject this proposal."
The GLA said it has commissioned a review of evidence on the impact of energy from waste on public health in the capital.
Dougie Sutherland, CEO of Cory Riverside Energy, said: "London faces challenges to its recycling and waste reduction targets, but incinerators are not the problem. Over two million tonnes of London’s non-recyclable waste is currently sent to landfill or shipped overseas, so there is a capacity gap that urgently needs investment.
"Our proposed Energy Park will play a significant part in addressing this shortfall and will also deliver a sustainable waste management solution for London, increasing renewable, low carbon energy generation and reducing greenhouse gas emissions. We will not have any detrimental effect on recycling rates, or the recycling targets set in adopted and emerging policy."
Last week, the Welsh Government announced an investigation into the potentially unlawful granting of planning permission for a waste incinerator in Barry.