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The administration was carried out by the Militair Gezag, literally the Military Authority. This authority was initially based in Brussels (Belgium), later in Breda and finally in The Hague. They had lower authority than the Supreme Allied Commander Allied Forces (General Dwight D. Eisenhower) leading the Supreme Headquarters Allied Expeditionary Forces (SHAEF), Mission to the Netherlands.
From Wikipedia:
De Nederlandse regering in Londen voorzag grote bestuurlijke problemen na de bevrijding van Nederland. Daarom werd het bestuur bij wet aan het daarvoor opgerichte Militair Gezag opgedragen. De juridisch geschoolde generaal-majoor mr. H.J. Kruls werd Chef van de staf van het Militair Gezag. De ministerraad passeerde daarmee de kandidaat van Koningin Wilhelmina; zij had haar schoonzoon Prins Bernhard voorgesteld. Het Militair Gezag werd opgericht op 14 september 1944 en ontbonden op 4 maart 1946. Kruls was gedurende deze hele periode Hoofd van het Militair Gezag.
Which means:
The Dutch government[-in-exile] in London foresaw large governmental problems after the liberation of The Netherlands. Therefore the governance was transferred to the Military Authority. The law-educated general-major mr. H. J. Kruls became Chief of the Military Authority. The council of ministers thereby bypassed by the candidate preferred by Queen Wilhelmina; she had proposed her son-in-law Prince Bernhard. The military authority was established on 14 September 1944 and was disbanded 4 March 1946. During the entire period, Kruls led the Military Authority.
Interior minister Louis Beel was at this time based in OisterwΔ³k.
The period is described in detail the book:
D.C.L. Schoonoord. Het Circus Kruls, Militair Gezag in Nederland, 1944 β 1946. Available online: PDF, 4.8 MiB, 890 pages (in Dutch).
There was also a College van Vertrouwensmannen, who had the task to represent the government between liberation and return of the government-in-exile.