Aglukkaq was named the Minister of Health on October 30, 2008, and is the first Inuk in Canadian history to be appointed to the Cabinet of Canada. Jack Anawak and Nancy Karetak-Lindell previously held parliamentary secretary positions, which are not part of the cabinet itself. Considerable public attention was focused on Aglukkaq during the 2009 swine flu pandemic where hundreds of Canadians were infected with the H1N1 virus. The Liberal health critic said that Aglukkaq was doing a "terrific job," and especially liked how the minister phoned all opposition critics to build consensus on the swine flu issue. Health Canada officials sent two dozen body bags, normally sent to hospitals, to a Manitoba First Nation. The move was criticized by Aglukkaq, the Liberal and New Democratic opposition parties in Parliament, and First Nations leaders. An investigation ordered by Aglukkaq found "no evidence of ill will or deliberate calculation," though First Nations representatives in Manitoba criticized the inquiry's report for downplaying the incident. Following the outbreak, Aglukkaq appeared on various television shows, including CBC News Network's Power and Politics with Evan Solomon, underlining the government's immunization plan. In 2009, the World Health Organization called for the elimination of artificial trans fats from the world food supply. Surveys at the time indicated that 90% of Canadian adults and children still exceeded the recommended daily limits on trans fats. A Health Canada analysis suggested a ban could prevent 12,000 heart attacks over 20 years, saving the health care system $9 billion. Internal documents showed Health Canada prepared to finally announce a full ban on trans fats, drafting the regulations and a press release, until the office of health minister Aglukkaq scrapped those plans. She later acknowledged the rules would be a burden on the food industry. Aglukkaq was criticised by public health officials for refusing to sign the Vienna Declaration on drug policy reform, which deemed "the evidence that law enforcement has failed to prevent the availability of illegal drugs unambiguous," and called for a "science-based approach" based on harm reduction strategies such as needle exchange programs and supervised injection sites, because the Declaration was in conflict with the Conservative government's long-established prohibition-centered approach.
On July 15, 2013, Aglukkaq was named Minister of the Environment, which includes responsibility for Parks Canada, the Canadian Environmental Assessment Agency and Environment Canada. In December 2014, Aglukkaq apologized for reading a newspaper while opposition parties asked the government about high food prices in the North during Question Period. During the 2015 Canadian federal election, Paul Okalik, Nunavut's Health and Justice Minister expressed his discontent with Aglukkaq's actions by reading a newspaper whenever Aglukkaq spoke at the Canadian Broadcasting Corporation election forum in Iqaluit. In the election, Aglukkaq lost almost half of her vote share from 2011 and was pushed into third place behind Liberal candidate and former Legislative Assembly speaker Hunter Tootoo and NDP candidate and former MP Jack Anawak. It was one of the larger defeats suffered by a member of Harper's cabinet. Aglukkaq ran again for the Conservatives in the 2019 Canadian federal election, and again came in third. The election was won by NDP candidate Mumilaaq Qaqqaq.
