Germany Launches Counteroffensive Against the Slovak Uprising

On September 19 German command replaced SS-Obergruppenführer Berger, who had been in charge of the troops fighting the Uprising, with General Höffle.

By that time Germans had 48,000 soldiers; they consisted of eight German divisions, including four from the Waffen-SS and one pro-Nazi Slovak formation.

On October 1 the rebel army was renamed the 1st Czechoslovak Army in Slovakia, in order to symbolize the beginning of the Czech-Slovak reunification that would be recognized by the Allied forces.

A major German counteroffensive began on October 17–18 when 35,000 German troops entered the country from Hungary, which had been under German military occupation since 19 March 1944. Stalin demanded that his advancing Second Ukrainian Front led by General Malinovsky be immediately diverted from Eastern Slovakia to Budapest. The western advance of Soviet forces came to a screeching halt in late October 1944, as Stalin's interests focused on Hungary, Austria and Poland before he was interested in Slovakia or the Czech lands. By the end of October, Axis forces (six German divisions and one pro-Nazi Slovak unit) had taken back most of the territory from the insurgents and encircled the fighting groups. Battles cost at least 10,000 casualties on both sides.

Insurgents had to evacuate Banská Bystrica on October 27 just prior to the German takeover. SOE and OSS agents retreated to the mountains alongside the thousands of others fleeing German advance. The rebels prepared to change their strategy to that of guerrilla warfare. On October 28, Viest sent London a message that said the organized resistance had ended. On October 30, General Höffle and President Tiso celebrated in Banská Bystrica and awarded medals to German soldiers for their part in the suppression of the uprising (claimed by some to have been done by Tiso as to save the lives of Slovak soldiers captured by German forces in the uprising, who were deported to concentration camps, and to save three Slovak cities from German bombardment).

Czechoslovak Army in Slovakia was established in Banská Bystrica. According to the decicion of Ministry of Defence in London, the insurgent units became part of Czechoslovakian Army. Jan Masaryk, Czechoslovak Minister of foreign affairs send a dispatch to Czechoslovak ambassador in Washington informing him of the National Uprising, in which partisans and regular people were fighting as regular units of the Czechoslovak army and asked “all three big allied countries” to acknowledge them as allied forces too. U.S. government did so on September 7, 1944, Soviet Union on October 11, 1944 and Great Britain in mid October.