Boyle and his American wife Caitlan Coleman were seized by the Taliban while hiking in Afghanistan in 2012, and then turned over to the group's affiliated militant Haqqani network in Pakistan.
The couple and their three children born in captivity were freed Wednesday in a Pakistani military operation triggered by US intelligence and are now back in Canada.
After landing in Toronto on Friday Boyle accused his captors of killing his baby daughter and raping his wife - accusations which the Taliban said were "fake".
Taliban spokesman Zabihullah Mujahid said Boyle and Coleman were never separated during their captivity, "precisely due to the fact that the mujahideen did not want to incite any suspicion", but he admitted a baby had died.
"During a period of detention an incident did take place when the woman became ill. The area was remote, no doctors were present and due to this severe condition, the woman had a natural miscarriage of a girl," Mujahid said in a statement.
The Haqqani group is headed by Sirajuddin Haqqani, who is also the Afghan Taliban's deputy leader.
The faction has long been suspected of links to Pakistan's shadowy military establishment.
Providing few details, Boyle said the death of his daughter and his wife's rape occurred in 2014.
That was two years after he and Coleman, then "heavily pregnant", were kidnapped in a remote Taliban-controlled area of Afghanistan.
He said they were in the war-torn country as "pilgrims" helping poor villagers when they were captured.
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