Second World War weapons washed up on Ulster beaches in 1993 were left by the Government to put the public in danger for more than six days after officials were informed.
Documents obtained by the Belfast Telegraph show Nigel Hamilton, now head of the Civil Service, believed the fiasco exposed a "major weakness" in the NIO's emergency planning procedures.
The phosphorous flares can burn the skin if exposed to air and have continued to sporadically appear on Ulster beaches after being dumped by the MoD in the Irish Sea.
In the days following the flares being washed up on several Ulster beaches in 1993, the MoD, NIO, police and fire brigade all washed their hands of the matter for various reasons.
Mr Hamilton, then at the DoE, described discussions among civil servants about the crisis as "buck passing" in a letter to an unspecified minister.
The letter, released by DoE under freedom of information, states: "No one in NIO or Northern Ireland departments was prepared either to accept responsibility for dealing with these flares or take necessary remedial action."
Mr Hamilton continued: "The risk of injury to individuals however, particularly on beaches at the weekend is such that some action must be taken on behalf of Government."
DoE only engaged a company to remove the munitions after "five to six days of prevarication by Government," because it became clear no one else was going to remove the flares.
Mr Hamilton asked the minister to contact the Secretary of State and initiate an "urgent, top level review of the emergency procedures and responsibilities, since this problem has revealed a major weakness in those arrangements".
In a 1993 letter to the chief executive of Moyle District Council the NIO said: "While their precise source is unknown, the flares definitely do not emanate from a UK military source."
The NIO letter blamed a "foreign military" or commercial waste for the flares.
A Government spokeswoman said following the crisis emergency planning procedures had been reviewed.
She said: "At the time of Mr Hamilton's 1993 memo the Lead Government Department principles were reviewed and guidance was issued to clarify the procedures for circumstances where a lead department was not immediately apparent."
The the spokeswoman added: "Emergency planning for all Northern Ireland Civil Service departments, including the NIO, continues to be updated and revised on a regular basis."