A briefing prepared for Canada's top military commander in 2011 outlined how the Foreign Affairs Department was examining the notion, under an anti-proliferation program established in the wake of the 9/11 attacks.
But a Foreign Affairs spokesman says there's no agreement to improve security around Islamabad's estimated 110 nuclear warheads, nor any consideration of one.
The relationship between the two nations grew increasingly frosty throughout the Afghan war with Pakistan's perceived support of Taliban militants who were killing Canadian troops in Kandahar.
The international community has grown uneasy as the government in Islamabad has amassed one of the fastest-growing nuclear arsenals in the world.
The defence briefing note, stamped secret and dated Nov. 9, 2011, claimed Foreign Affairs was "working to advance bilateral co-operation" with Pakistan on nuclear trafficking, training and other regulatory issues.
"Bilateral relations between Canada and Pakistan are modest," say the documents, obtained by The Canadian Press under the access-to-information law.
"However, (Foreign Affairs) is presently working under the auspices of Global Partnership Program to establish a nuclear security co-operation program with Pakistan. The initiative would improve diplomatic relations and enhance the security of Pakistan's nuclear assets."
But it is something officials now tersely deny.
Canada "does not have a bilateral agreement with Pakistan to enhance the security of its nuclear assets, nor is it in any way contemplating negotiating one at this time," Foreign Affairs spokesman Ian Trites said in an email.
In a separate email, a spokeswoman for National Defence, Elana Aptowitzer, described the briefing as "erroneous."
All of it strikes Canada's former high commissioner to Pakistan as strange.
Louis Delvoie said he's not sure what is driving Ottawa's thinking on the issue.
The fellow Commonwealth country has been eager to strike a civilian nuclear energy deal, similar to one Canada signed with longtime rival India in 2009. It has also lobbied Ottawa to drop the weapons technology ban issued in 1998 after Islamabad set off its first nuclear test.
A network established by Abdul Qadeer Khan to build nuclear weapons for Pakistan has since been shown to have smuggled technology and designs to Iran, Libya, North Korea and possibly Syria.
The theft or diversion of nuclear weapons material to terrorists has been a major pre-occupation of Washington since 2001, and the U.S. has poured $100 million into improving security at the erstwhile ally's storage sites.
Even though the Harper government is not prepared to offer assistance, Trites said Canada "remains deeply concerned with proliferation risks associated with the Pakistani program."
If that statement is taken at face value, Ottawa's lack of engagement on such a crucial issue is hard to understand, said Delvoie, who now teaches at Queen's University in Kingston, Ont.
"If the notion is to beef up Pakistan's safe, secure storage of nuclear technology then I think there is much to be said for that," said the former diplomat.
When they developed nuclear warheads, neither India or Pakistan had the sophisticated safeguards of either the U.S. or the Soviet Union. Equally concerning, Islamabad is not a signatory to the Nonproliferation Treaty.
"With their civilian nuclear programs, both countries have had blips," said Delvoie.
"Anything that can be done to make these things more secure, and avoid misappropriation by third parties, or the misuse of them, would all be to the good."