Udo Münch took early retirement after it emerged that police computers were used in unauthorised searches for details of two prominent personalities including a far-left politician, who subsequently received threatening letters and emails.
The messages were signed “NSU 2.0”, a reference to the German neo-Nazi cell National Socialist Underground that committed a string of racist murders in the 2000s.
While far-right extremism was once thought to plague mostly eastern states, Hesse was shaken last year by the murder of pro-migrant politician Walter Lübke at the hands of a neo-Nazi.
It was also in a city in the region — Hanau — where a man gunned down nine people of foreign origin in February this year.
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The row entangling Hesse's police force came as German law enforcement services are under close scrutiny over far-right extremism in their midst, a debate that has also been amplified by the Black Lives Matter protests in the United States.
Germany's defence minister last month ordered the partial dissolution of the elite KSK commando force over right-wing extremism.
The Military Counter-Intelligence Service (MAD) has said some 600 Bundeswehr (German military) soldiers are suspected of right-wing extremism, including 20 in the elite unit.