Bavarian state premier Horst Seehofer, head of the conservative CSU party, had openly clashed with Merkel at the height of the mass migrant and refugee influx in 2015.
More than one million people have since claimed asylum in the EU's biggest economy, a move that won Merkel much international praise but also sparked a harsh xenophobic backlash.
As border closures in the Balkans and an EU-Turkey agreement have sharply reduced the influx, Merkel's popularity has recovered and she is seen as the favourite to win the election.
Speaking to public broadcaster ARD, Seehofer said: "The situation has changed, and the position in Berlin has changed," pointing to tougher asylum laws and EU border protection measures.
"We now have markedly less immigration than at the time I made those comments," he added.