It comes after Judge Claudio Bonadio asked to partially lift Ms Fernández’s immunity as he investigates bribery allegations during her presidency.
Ms Fernández denies any wrongdoing.
In a defiant speech on Wednesday, the senator – who has immunity from imprisonment, but not prosecution – described the investigation as “shameless”.
She told senators she regretted “nothing” – apart from “not having been intelligent or open enough to convince and persuade people that what we were doing – with its mistakes and successes – improved the lives of millions”.
She also complained about becoming “the first elected senator to be searched”.
However, on Wednesday, she still voted for her immunity to be lifted to allow the search of her three properties to go ahead – and instructed her colleagues to do the same.
Thursday’s search relates to the so-called notebook scandal, which relates to a batch of records kept by Oscar Centeno, a driver for a public works official, over a 12-year period.
In the notebooks, Mr Centeno writes about delivering bags of cash from construction bosses to government officials, which prosecutor Carlos Stornelli says totalled some $160m (£125m).
Mr Centeno’s notebooks include a reference to money exchanging hands at the home shared by Ms Fernández and her late husband, Néstor Kirchner, as well as the presidential residence and government headquarters. However, none of this has been proven.
More than a dozen people, including businessmen and former government officials, were arrested after the notebooks were handed to authorities by La Nación newspaper earlier this year.
Ms Fernández is also under investigation in another five cases. She denies all allegations, and says she is the victim of a political witch hunt.