The petition, organised by worshippers in the borough of Newham, has drawn the signatures in 10 days. The mosque scheme includes an Islamic garden, school and prayer space for 70,000.
It has been criticised by the Muslim community who fear the involvement of Tablighi Jamaat, an ultraorthodox sect, behind the proposal.
Moderate Muslims say allowing the sect to build the complex will stoke community tensions. The petition warns the mosque could provide a recruiting ground for terrorists.
The sect preaches a strict interpretation of Islam which has been adopted by extremists and terrorists.
Asif Shakoor, chairman of the Sunni Friends of Newham, said they wanted all Muslim groups to be equally represented at the proposed place of worship.
Ruth Kelly, the Communities and Local Government Secretary, is aware of the petition. She has the power to subject the scheme to a public inquiry.
Newham council signed a memorandum of agreement in 2001 with the charity behind Tablighi Jamaat, the Anjuman-E-Islahul Muslimmen, which stated there would be “no objection in principle to … a major new, high-quality mosque”.
But a leaked FBI document, obtained by the American news media in 2001, raised fears that al Qaeda was using membership of the Tablighi Jamaat “as cover… to network with other extremists in the US”.