Mr Khan, Labours candidate in next months election, also called for a strategic review of river crossings and public transport connections east of Tower Bridge and criticised current mayor Boris Johnsons proposals as piecemeal.
His comments on the Silvertown tunnel mean that his Conservative rival Zac Goldsmith is the only leading mayoral candidate to fully back the scheme. Both Liberal Democrat Caroline Pidgeon and Green Party candidate Sian Berry oppose it.
Last month, it wasrevealed that Mr Goldsmith was the only candidate to support Mr Johnsons plans for other tunnels in the capital.
Mr Khan said: We desperately need additional river crossings east of Tower Bridge to support and open up new development sites for affordable homes and to improve connectivity between north and south London.
Plans as they stand for the Silvertown Tunnel do not fully take into consideration the importance of greener transport, and imposing a toll is in many peoples minds a tax on east and south east Londoners.
We need a proper joined up review, looking at river crossings and improved public transport connections east of Tower Bridge, but in a strategic fashion, not piecemeal like the current mayor.
TfLs proposals for the Silvertown Tunnel, which would follow the route of the cross-Thames cable car, would include user charging on both the new tunnel and the existing Blackwall Tunnel to pay for the scheme and keep traffic levels down.
The proposed tunnel is part of a wider package of Thames crossings set out by TfL last December in Connecting the Capital.