The woman's estranged husband flew out of the country to Kenya on Saturday shortly after dropping off the children, aged nine and 13, at the home of a friend and police have alerted Interpol to try and track him down.
The woman was today in Christchurch Hospital in stable condition with severe head injuries while the dead man's body remained at the Burrows Place, Ilam, house as police tried to piece together what happened.
Friends raised the alarm after becoming concerned at not seeing the woman.
Police broke into the house last night and found the couple in a bedroom - the man dead on the floor and the woman lying injured on a bed.
"We are unsure what has occurred between late Friday and Sunday morning ... there are indications that the husband may be involved," the officer in charge, Detective Inspector Greg Williams, said.
The dead man is yet to be formally identified, but police say he was a close friend of the injured woman.
Mr Williams said a weapon was probably used in the killing, but would not say what it was or whether police had recovered it.
The mother and her two children moved to the house in Burrows Place four weeks ago after she separated from her husband.
The Kenyan couple had lived in New Zealand for many years.
The injured woman's husband is understood to have arrived in Kenya this morning.
Mr Williams said police were working with Interpol and Kenyan authorities to try to locate him. But they may have difficulty in bringing him back to New Zealand because there is no extradition agreement between the two countries.
Mr Williams said it was unclear what the relationship between the woman and the dead man had been beyond a friendship.
Police had not yet been able to speak with the woman, who was in a serious but stable condition at Christchurch Hospital, but had spoken with the children.
"Supporting these kids whose mum's clearly not well in hospital and father has now left the country, is our key focus, just trying to support them through this," he told Radio New Zealand.
Mr Williams said police had been called to the address two weeks earlier when the husband and wife had an argument regarding their separation, although there had been no physical violence on that occasion.
