The decision was taken "in response to the crisis in the organisation and in defence of the general interest of Spain," the National Sports Council (CSD), which is the government agency responsible for sport, said in a statement.
The move follows months of scandals after a corruption investigation sparked by an unsolicited kiss from former RFEF chief Luis Rubiales on player Jenni Hermoso at the on pitch awards ceremony for Spain's women's World Cup success in Sydney.
"The Spanish government has taken this decision in order to correct the serious situation that the RFEF is going through and to allow the organisation to begin a period of regeneration," the CSD said.
"This Commission for Supervision, Normalisation and Representation will be headed by independent persons of recognised prestige."
