The 17-year-old disappeared six months ago following a trip to Pakistan where she had been introduced to an arranged marriage suitor.
Her decomposed body was positively identified only yesterday after it was discovered in the River Kent in Sedgwick, near Kendal.
Detective Chief Inspector Geraint Jones said there was evidence that her body was concealed in undergrowth to avoid detection.
He added: "A post-mortem examination of Shafilea’s body has not been able to provide a precise cause of death.
"However, following intensive scene examination by forensic experts, it is evident Shafilea’s body had been concealed at that location for some months and perhaps from the night she went missing.
"This is therefore now a murder inquiry being led by the Cheshire Constabulary, supported by our colleagues in Cumbria."
Police have not ruled out the possibility that her death was the result of an "honour killing", but her parents today denied any involvement in her death.
A statement read on behalf of Ifitkar and Farzana Ahmed by their solicitor said: "They wish to confirm once more that they strenuously deny any direct or indirect involvement in their daughter’s untimely demise."
They were arrested before Christmas on suspicion of her kidnap, but were released without charge pending further inquiries.
Shafilea, from Warrington, Cheshire, drank bleach in an apparent attempt to kill herself while in Pakistan. She needed extensive hospital treatment on her return to Britain.
Mr Jones said: "The phrase ’honour killing’ is not something I have introduced but we have to investigate the possibility that Shafilea was killed because she has not consented to something."
Poignant song lyrics written by Shafilea were read at a press conference by Coronation Street actress Shobna Gulati in December. Ms Gulati said the teenager was trapped between two worlds.
In the poem, Shafilea said: "I was like a normal teenage kid. Didn't ask 2 much. I just wanted to fit in."
Ms Gulati said: "I think she is definitely looking as though she is trapped between two cultures. She wants to express something and is unable to do that."
