He published, anonymously, a paper on the findings of the investigation, which is considered an important historical document due to the fact that the Nazis destroyed all official reports from the inquest after 1933.

For this reason, he was dismissed from government service after the Nazi takeover in 1933 and had to escape to Austria, and from there, in 1934, to Switzerland, where he worked as a freelance writer.

When his party decided to leave the coalition with the Christian Social Union (CSU), he opposed this move and temporarily lost influence within the SPD, resigning from his ministerial post.

While a social democrat, Hoegner was not a doctrinaire socialist, and he always preferred a common-sense approach to politics and the economy, rather than radical theories.

He considered being a social democrat to be wholly compatible with Christian ethics and values—an important factor in the traditionally conservative and Catholic-dominated state of Bavaria.