Considerable public attention was focused on Aglukkaq during the 2009 swine flu pandemic where hundreds of Canadians were infected with the H1N1 virus.

[14] 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.

[15] 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.

Surveys at the time indicated that 90% of Canadian adults and children still exceeded the recommended daily limits on trans fats.

[citation needed] 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.

[16][17] Aglukkaq was reelected in 2011 with nearly 50 percent of the vote, defeating a field of challengers which included former Premier of Nunavut Paul Okalik, who ran as the Liberal nominee.

On August 23, 2012, Prime Minister Stephen Harper announced that Aglukkaq would serve as chair of the Arctic Council when Canada assumed the Chairmanship from Sweden in May 2013.

[24] 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.