Authorities were searching for more than a dozen Rolex watches President Boluarte had allegedly not declared.
The investigation began after a news report drew attention to luxury watches she wore at public events, dating from when she took office in December 2022.
Peru's government described the raid on Saturday as "disproportionate and unconstitutional".
"The political noise that is being made is serious, affecting investments and the entire country," Peruvian Prime Minister Gustavo Adrianzen wrote on X, formerly Twitter.
The government comptroller announced earlier this month it would review Ms Boluarte's asset declarations from the past two years.
Speaking last week, Ms Boluarte insisted she entered government "with clean hands" and that she would "leave it with clean hands".
