João Goulart was fully aware he could be overthrown by the military and took measures to contain potential officer conspiracies. From below he had leftist sergeants, and from above, the "military apparatus": upper echelons had been stacked with generals deemed loyal, the work of his ally Assis Brasil in the Military Cabinet. Goulart's subordinates had bold ideas in 1963, after the return of presidentialism, when he attempted to declare a state of emergency and unseat the rightist governors of Guanabara and São Paulo (and potentially, the leftist governor of Pernambuco). They had planned a paratrooper abduction in Guanabara, but the need to find a colonel who'd do it without written orders delayed it until it could no longer be carried. But the state of emergency could not be declared due to opposition from the left. This scheme's failure was a factor in Goulart's turn to the left in 1964.
Potential enemies were left in powerless positions or bureaucratic limbo. Mourão Filho was an important exception, but even he formally responded to a legalist superior.
Each branches of the Armed Forces had its own Minister. The War (i.e. Army) Ministry was under Jair Dantas Ribeiro. Paulo Mário da Cunha Rodrigues commanded the Ministry of the Navy after his predecessor resigned in the wake of the sailors' revolt; he was close to the communists. The Air Force was under the unremarkable Anísio Botelho. All three had to be sacked after the rebels took over as they did not switch sides.

Within the Army the higher level was armies and military commands, both under four-star army generals. They were deemed to be under safe hands but that was proven not fully correct. They commanded Military Regions and Divisions, both under three-star division generals whose loyalty varied. In Minas Gerais the divisional and Military Region commands functioned as one. Not all states had divisions. There were 6 of infantry and 3 of cavalry. Rio Grande do Sul alone had the 3rd and 6th Infantry and the 1st, 2nd and 3rd Cavalry; this disproportionate concentration is a legacy of the military's historical Platine focus. However the garrison in Rio de Janeiro/Guanabara was arguably just as strong as it was well-staffed, heavily armed and could count on paratroopers, marines and a lot of air/naval support. A level below were two-star brigade generals who commanded important units (like the paratrooper brigade) and the Divisional Infantry and Divisional Artillery Commands. Fighting strength was in the three-battalion regiments, three by infantry division, as well as in apparently separate caçadores (light infantry) battalions.