In a separate emergency decree, the defence procurement agency was ordered to answer to President Recep Tayyip Erdogan instead of the defence ministry, in a move widely viewed as a further expansion of his powers.
Turkey's intelligence service (MIT) also came under Erdogan's control in August.
A total of 2,756 people including academics, soldiers and military personal were removed from different bodies including the interior, foreign and defence ministries, according to the Official Gazette.
17 Turkish institutions were also ordered to close, including two newspapers and seven associations.
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More than 140,000 people including judges, lawyers and academics have been sacked or suspended since a failed coup in July last year, while some 55,000 people have been arrested over suspected links to US-based Islamic cleric Fethullah Gulen and the coup attempt.
Turkey claims Gulen and his Hizmet (service) movement, which it calls the "Fethullah Terrorist Organisation", ordered and conducted the attempted coup.
Gulen, who has lived in self-imposed exile in Pennsylvania since 1999, denies any links to terrorism and the failed putsch.
But on Sunday, Prime Minister Binali Yildirim said Turkey would hire 110,000 public sector employees in 2018, including 20,000 teachers, 36,000 health sector workers and 15,000 people to work for the justice ministry. Thousands of judges and prosecutors have been sacked in the purges.
"Thus in the ministries and state departments, there will not be a problem of "'disruption due to lack of personnel'," Yildirim said in televised comments.
The co-leader of the main pro-Kurdish opposition Peoples' Democratic Party, Selahattin Demirtas, is among those detained on terrorism charges, something he denies.