The Department for Culture, Media and Sport (DCMS) will continue to fund two non-national museums - the Horniman Museum and Gardens and the Geffrye Museum in London.
In October 2010, the DCMS said that it was looking to relinquish responsibility for the two museums and pursuing alternative sponsors.
Following discussions about alternative options, including a possible transfer to Arts Council England, the DCMS have decided not to pursue any alternative sponsorship options and for the museums to remain with the department.
The Horniman Museum and Gardens in South East London specialising in anthropology, natural history and musical instruments, while the Geffrye Museum in East London specialises in the history of the home.
A spokesperson for the DCMS said: "We are fully committed to building on the success of both museums and ensuring their future success."