Putin was scheduled to travel to Germany for talks with Merkel Sunday and Monday.
Both German and Russian officials said Merkel will ask him about the unannounced inspections, which have been conducted across Russia and have affected some German NGOs, RIA Novosti reported.
German officials have said the inspections are impairing relations between the two nations.
"I don't know how sharp the nature of the exchange of opinions will be but you know what the mood is ahead of the visit, and it is clear the chancellor will raise the issue of NGO inspections," Russian presidential aide Yury Shashkov told RIA Novosti Friday.
Russian activists say the inspections, which began in February, are intended to scare NGOs into complying with a controversial law that labels them as foreign agents.
Putin said last week the inspections were "routine measures linked to the desire of the law enforcement agencies to bring the activities of organizations in line with the law."