The information from the Money Laundering Reporting Office Switzerland (MROS) had been reported in the Swiss-German press.
The money-laundering probe concerns possible corruption "for which Viktor Yanukovych and his entourage could be involved," said the spokeswoman for the federal department in Bern.
The pro-Moscow ex-Ukrainian leader and his entourage, whose assets were frozen by the Swiss government two weeks ago, are already being investigated by the canton of Geneva.
Ukrainians, grappling with an economy on the brink of default, were shocked by the breathtaking opulence of Yanukovych's vast country estate which was flung open for all to see when he went into hiding and fled to Russia.
Swiss newspapers SonntagsZeitung and Le Matin Dimanche reported that boxes of Swiss luxury watches were found in the home.
Brands included Chopard, Cartier, Rolex and Franck Müller.
The boxes were empty but certificates of guarantee showed that some of the timepieces were bought in Switzerland, notably in the mountain resort town of Gstaad in the canton of Bern, according to the reports.
The canton of Geneva is reportedly looking into deposits made to a Credit Suisse account.