The move comes amid Chadha's prolonged silence on matters related to the AAP, and his absence from several public events led by AAP supremo Arvind Kejriwal.
Banerjee said the EC had stripped her government of authority by transferring senior officials and posting its own officers, adding the poll panel could "no longer evade responsibility."
The 11 resolutions spread across areas like governance, identity, healthcare, infrastructure development, industrialisation, agriculture, rural and urban development, climate change and security.
The apex court directed the Election Commission of India to entrust the enquiry or investigation into the incident to either the CBI or NIA and submit a compliance report.