Sepa said yesterday that a timetable had been agreed with the Defence Infrastructure Organisation (DIO) to carry out decontamination work at Dalgety Bay in Fife.
More than 200 radioactive particles have been found on the beach, which was once home to a wartime airfield.
It is thought that the area became contaminated when planes were dismantled there and used for landfill, with particles from radium dials slowly eroding into the ground.
The row over who is responsible for the clean-up had led to a stand-off between Sepa and the MoD, but this has now been resolved.
The details of the plan will be made public following a meeting of the Dalgety Bay Forum on March 2.
Former Prime Minister Gordon Brown, the local MP, welcomed the announcement but said that defence officials needed to go further.
He said: "I and the community council are clear that we need a full statement of the discovery of radiation particles in the area."
Radioactive material was first detected at Dalgety Bay in 1990.
David Olney, of DIO, added: "This investigation plan represents a tangible example of DIO's commitment to assist and support Sepa and the Expert Group in understanding the situation at Dalgety Bay and determining what needs to be done and by whom."