At least 70 percent of the Fijian population who had Covid-19 when they died were also suffering from a chronic disease, health authorities said.
And the majority of these cases were non communicable diseases or NCDs.
Health Secretary Dr James Fong said the government would now change its focus to addressing the NCD situation in earnest.
He said this was important because the most recent medical data pointed to the need to protect the most vulnerable in Fiji.
Dr Fong said the shift in strategy meant the government would need to keep better track of patients on record and keeping the rest of the population healthy.
"Our data show that we are through the worst of this third wave," he said.
"Our employers can also vouch for this given the decreasing of Covid-related absences from work.
"All that said, our Covid-safe measures must continue in the near term to protect those most vulnerable.
"We have seen relatively low rates of hospitalisations and deaths in this wave due to our high rate of vaccination and have not had to create any extra space in our treatment facilities or mortuaries," Dr Fong said.
But among the fatalities recorded, Dr Fong said there was a clear trend "most are unvaccinated, suffer from serious comorbidity, and die while at home.
"This trend tells us that the next stage of our response involves a more holistic view of the medical realities the nation faces."
NCDs worsen Covid-19 and inflict a far higher toll on the country "than the virus ever could."
According to Ministry of Health records, NCDs are already responsible for more than 80 percent of deaths annually since July 2020.
"After nearly two years of non-stop Covid-19 coverage, I fear that this issue - which is by far and away from the number one killer of our people - has become secondary in our national discourse.
"But the suffering it creates is not second to any threat our people face to their well-being."
In 2020, 5,700 Fijians died from NCDs like diabetes, stroke, heart disease, and the ministry of health has listed tobacco use, Physical Inactivity, Unhealthy diet and alcoholism as the major causes of NCDs in Fiji.
"NCDs are deadly on their own - but Covid-19 can turn them into more efficient killers.
"NCDs and other comorbidities also complicate our ability to precisely determine the causes of death.
"It may be that someone died with Covid, but not from it - but because most deaths have been at home that can be very difficult to determine."
While the MOH's policy has been categorised as Covid-19 deaths - those NCD patients who were killed by the virus - Dr Fong said it was the urgency of identifying, treating and preventing NCDs was paramount.
The Government said it acknowledged that Covid-19 is endemic in Fiji and so it would focus in promoting better health-seeking behaviour to build people's resilience to the virus.
Pushing healthy eating and active lifestyle messages, the MOH said it would divert attention to improving digital records of patients in order to improve their access to services which would help them maintain life.
Fiji loses over $400 million annually in productivity because of resources spent and lives lost to NCDs, Dr Fong said.
"This all goes to show how and why our perception of health priorities needs to change.
"In much the same way we needed a whole of society response to deal with Covid-19, we need an effective whole of society response to deal with NCDs," Dr Fong said.
"Working with key partners WHO, UNDP, UNICEF, World Bank, and other organizations such as Diabetes Fiji Inc, Fiji Cancer Society, Medical Services Pacific, Empower, Lifeline Fiji, National Committee On Preventing Suicide, Substance Abuse Advisory Council, we have evolved a network of avenues to help to provide prevention and care services for NCDs."
Fiji has had more than 60,000 cases of Covid-19, with the death toll at 791 since March 2020. There are 1,980 active cases in isolation.