In 1988 Kujat passed the 72nd course of the NATO Defense College in Rome and was promoted an Oberst in October 1988. In 1989 he became a referent of the German Representative at the Chairman of the Military Committee in Brussels, Branch Chief (Nuclear and Global Arms Control) at the Federal Ministry of Defence in 1990 and Chief of Staff and Deputy German Military Representative to the NATO Military Committee and the Western European Union, Brussels, in 1992–95.[3]
In 1996 Kujat became the Director of the IFOR Co-ordination Centre (ICC), Supreme Headquarters Allied Powers Europe (SHAPE), Mons, Belgium and in October Deputy Director of the NATO International Military Staff in Brussels.
On 10 November 1998, Kujat, now a Generalleutnant, became the Director Policy and Advisory Staff to Rudolf Scharping, the German Minister of Defence, Berlin and on 1 June 2000 the Chief of Staff of the Federal Forces. In 2002 Kujat became the Chairman of the NATO Military Committee until his retirement on 17 June 2005.
Since July 2016, Kujat is a member of the Supervisory Board of the Berlin-based Research Institute Dialogue of Civilizations[4] (DOC), allegedly financed by Vladimir Yakunin.[5] It ceased operation in 2021.
Some conservative German media (Bild-Zeitung, Die Welt) criticized Kujat for his pro-Russian views in German TV talk shows,[6][7][8] his praise for Russia's bombing raids in Syria were met with misgiving by the German Federal Government.[9]
While former high ranking officers of the Bundeswehr are meant to refrain from political comments, Harald Kujat made several public statements in context with the Russian invasion of Ukraine of 2022 and the role of western nations in it. He claimed that former British prime minister Boris Johnson prevented a "peace treaty" between Ukraine and Russia in 2022. Former fellow Bundeswehr generals, who had worked with Kujat, expressed in mid 2024 irritation with his pro Putin remarks, accusing him of selective perception of facts, like ignoring the defacto destruction of several Russian divisions in the battles around Kharkiv, the loss of Russian control over parts of the Black Sea and the inablility of the Russian forces to defend Crimea from Ukrainian airstrikes. Klaus Naumann concluded in July 2024, that, after his time negotiating with Russia in the late 1990s during the Kosovo War, Kujat had apparently lost touch and did not realize the changes in Russia in the past decades. When confronted with criticism, Kujat quit an interview with the Neue Zürcher Zeitung in Neuruppin in 2024.[11]