On 12 April 2016, Magufuli conducted his first foreign visit to Rwanda, where he met his Rwandan counterpart Paul Kagame and inaugurated the new bridge and one-stop border post at Rusumo. Magufuli also attended the memorial of the 22nd anniversary of the Rwandan genocide.
In July 2016, Tanzania banned shisha smoking, with Magufuli citing its health effects among youth as the reason. In March 2017, Tanzania banned the export of unprocessed ores, in an effort to encourage domestic smelting. In January 2018, Magufuli issued a directive ordering the suspension of registration for foreign merchant ships, following recent incidents surrounding the seizure of overseas shipments of illegal goods (particularly drugs and weapons) being transported under the flag. Tanzania and Zanzibar had gained reputations for being flags of convenience.In the same year, He introduced a fee free education for all the government schools in 2016.
Magufuli's government has been accused of repressing opposition to his leadership, including laws restricting opposition rallies, the suspension of the Swahili-language Mawio newspaper in 2016 for publishing "false and inflammatory" reporting regarding the nullification of election results in Zanzibar, threatening to shut down radio and television stations that do not pay licence fees, and a 2018 bill requiring blogs and other forms of online content providers to hold government licenses with content restrictions. A devout Catholic, he has been publicly criticized by the Conference of Catholic Bishops of Tanzania for taking measures that suppress constitutional freedoms and, in the view of the bishops, represent a threat to national unity.
People convicted of same-sex liaisons in Tanzania can be jailed for up to 30 years. In October 2016, the Tanzanian government banned HIV/AIDS outreach projects and closed US-funded programs that provide HIV testing, condoms and medical care to the gay community. The countrywide closure of private HIV clinics began soon afterward. In late 2018, Magufuli initiated a nationwide crackdown, threatening to arrest and deport anyone campaigning for gay rights and making it difficult to find a lawyer who will defend cases of violence against LGBTQ people.