The top bureaucrat at Natural Resources warned the minister last year about possible risks to the government's plan to use cyclotrons and linear accelerators to make a key medical isotope once the Chalk River reactor is shut down.
CBC obtained a copy of a memo, written by the department's deputy minister to Greg Rickford in January 2014, under an Access to Information Request.
Currently, most of the world's supply of a medical isotope used to diagnose and treat some types of cancer and heart disease is produced at five nuclear reactors around the world, including the aging National Research Universal reactor in Chalk River, Ont., which was supposed to wind down next year.
A number of research facilities in Western Canada and at the University of Sherbrooke in Quebec have successfully made the isotopes without need of a nuclear reactor, promising a more reliable supply of the isotopes.
But the memo says the most "significant" risk to moving ahead with the new technologies is "obtaining the necessary health regulatory approvals by 2016."
Those approvals must be made by Health Canada and the U.S. Food and Drug administration.
CBC News asked for an interview see what, if anything, has changed in the 18 months since the memo was written.
The department refused to offer anyone to answer questions, but in a statement said: "Project proponents continue to work with Health Canada and the Food and Drug administration in the United States to advance health licensing requirements."
In an email, Health Canada says it has approved only two trial applications for the use of isotopes made in cyclotrons so far. But it has not received any other applications from other facilities either.
Isotopes in tight supply in 2017
The memo also refers to the global supply of isotopes after the NRU's license was initially supposed to expire, in October 2016.
It says the global supply should be sufficient from 2015 to 2020, even without the Chalk River reactor. But, it adds, "2017 will be a year with little excess capacity to deal ith any unexpected reactor outages."
This may be the reason behind the federal government's announcement this spring to extend the life of the Chalk River reactor to March 31, 2018.
The reactor was first brought into operation in 1957, but it has in recent years needed almost half a million dollars in repairs, and was unexpectedly shut down for months in 2009.
That disruption to isotope supply led the Harper government to begin to look for alternative technologies to make isotopes.
Since then the federal government has invested $60 million into research at a number of facilities, including Canada's national particle and physics lab, known as TRIUMF, the Prairie Isotope Production Enterprise and the University of Alberta in conjunction with the University of Sherbrooke.
The Canadian Nuclear Safety Commission still needs to approve the extension of the Chalk River license to 2018.
The documents obtained by CBC also lay out in more detail how the federal government wants the new isotope production to work, once the NRU is finally decommissioned in three years.
Isotopes made in cyclotrons have a shorter shelf life than those made in the nuclear reactor, creating challenges for the transportation of effective isotopes.
A map shows that under the federal government's plan, there would be an isotope production facility in every almost every province, and a range for how far they could be distributed by land and air.
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