Prime Minister Justin Trudeau acknowledged problems at the Public Health Agency on Tuesday, after two top doctors criticized an erosion of funding and scientific capacity for hindering its ability to confront a pandemic.

Mr. Trudeau put much of the blame for the problems on the previous government, saying structural changes and funding cuts implemented by the Conservatives prior to 2015 are at the heart of the matter.

“We all knew that under the previous Conservative government there were massive cuts to science, there was marginalization of scientific voices, there was a putting-aside of experts in an attempt to cut the budget, cut the deficit at all costs, on the backs of Canadians,” Mr. Trudeau said.

The government has made considerable investments in science since then, he said.

However, doctors and epidemiologists inside Public Health say the problems were never fixed. Even though the Liberals opposed the Conservatives’ moves at the time – such as the creation of a government-appointed president to run the agency – they say the Trudeau government allowed them to persist. These include an influx of senior government officials from other departments who lack a sufficient understanding of public health.

The department has been beset by problems in recent months, including a controversy over the mishandling of the country’s pandemic early warning system, shortages in the emergency stockpile and allegations that scientists had to “dumb down” reports for senior managers.

A Globe and Mail investigation in July reported that the country’s pandemic surveillance system, a highly specialized unit known as the Global Public Health Intelligence Network, or GPHIN, was effectively silenced in 2019. That ill-timed decision came as the department, having not faced an outbreak threat in several years, sought to reallocate GPHIN’s resources for other projects that didn’t involve pandemic preparedness.

Such problems are symptomatic of a larger ailment at the agency, public-health experts say.

This week, two top doctors spoke out about what they saw as persistent underfunding of the agency, and an erosion of scientific capacity within its ranks. The government was warned years ago that Public Health was destined for problems if certain structural matters were not addressed, they said.

Perry Kendall, who preceded Bonnie Henry as B.C.'s provincial health officer from 1999 to 2018, and Paul Gully, who filled senior roles at Health Canada for 14 years and was a former deputy chief public-health officer, called on the government to address the structural problems.

“We are of the view that long-term deficiencies of expertise and funding prevent the Public Health Agency of Canada from fully carrying out its intended and necessary role,” said Dr. Kendall, who warned of such problems during federal hearings in 2014.

The decision to give control of budgets and program planning to the president, a government appointee with no background in public health, leaves the department prone to short-term thinking, Dr. Kendall said. This is a particular risk between major outbreaks, when there are no immediate threats and the temptation to move funds elsewhere is heightened, or the agency’s mandate is expanded into new areas. The "short-sighted” handling of the pandemic intelligence system is just one example, Dr. Kendall said.

Their comments echo those of another respected voice in public health, former chief public-health officer David Butler-Jones, who warned this year that the agency had, over time, “replaced public-health managers and analysts with generic public servants.” As a result, “Resources, expertise, and capacity have been reduced, and expertise positioned further away from where organizational decisions are made.”