Documents obtained by The Canadian Press under the Access to Information Act show the warden of Millhaven Institution, where Khadr is in maximum security, approved the interview request made by the news agency in January, only to be overruled.
The refusal came from the office of Public Safety Minister Vic Toews to Correctional Service Canada, records show.
Under normal procedure, the warden of an institution makes the final call on granting a reporter access to an inmate, subject to a CSC policy known as Commissioner's Directive 022.
Among other things, the directive requires agreement from the prisoner to talk to the reporter, and any interview cannot pose a security threat.
The documents show Prime Minister Stephen Harper's own department immediately flagged the initial interview application, and asked to be kept in the loop.
"We'd be interested if anything develops on the (request)," Christopher Williams, a senior analyst with Privy Council Office, wrote in an email to Correctional Service Canada.
In this case, Millhaven Warden Kevin Snedden approved a telephone interview with Khadr. Documents show regional headquarters supported his decision.
"Following the warden's detailed assessment of the request against Commissioner's Directive CD-022, it was concluded that the request complies," Christa McGregor, senior media relations adviser, wrote in an email Feb. 22 to senior ministry and ministerial staff in Toews' office.
Within 90 minutes, however, the request was nixed.
"This interview is not approved," Julie Carmichael, Toews' director of communications, responded in a terse internal email.
The decision to overrule the warden took Correctional Service insiders by surprise, prompting a further flurry of emails that reached the highest levels of the ministry.
A public servant familiar with the file, who insisted on anonymity out of fear of government retribution, said what had happened was highly unusual.
The interview request was "subjected to significant and extraordinary scrutiny from CSC's national headquarters and overt political interference," the person said.
"The warden approved of the interview taking place — and approved again after being told to reassess — before finally, and after much 'off-line' conversation with direct pressure from headquarters and the minister's office, denying the request."
It was not immediately clear what role the cabinet office played.
Wayne Easter, a former Liberal solicitor general, expressed surprise at Toews' involvement, saying he couldn't think of an instance where something similar had happened during his time in office.
"It's very much overstepping the bounds of the minister's jurisdiction," Easter said. "As long as the protocols are met, (the interview) should go ahead."
The Toronto-born Khadr, 26, has been housed in Millhaven west of Kingston, Ont., since his transfer last September to Canada from Guantanamo Bay, where he had already spent 10 years behind bars.
Khadr had pleaded guilty before a widely discredited military commission in October 2010 to five war crimes — among them killing a U.S. special forces soldier — committed as a 15 year old in Afghanistan. He was given a further eight years behind bars.
In its refusal — denounced by Khadr's lawyer as Conservative government "propaganda" aimed at demonizing him by keeping him out of the public eye — Correctional Service Canada cited the commissioner's directive for rejecting the interview.
It said access could pose a security risk or be disruptive, and would undermine his correctional plan.
Nowhere in the records is there any indication the warden initially found those to be issues.
Asked to comment on the minister's interference in the process, Carmichael would only say Toews expects consideration of interview requests to take into account the "nature of the offences" of which the individual has been convicted.
All requests to talk to other bureaucrats or political operatives involved were denied, with media relations officials citing the Privacy Act.
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