The stock plunged more than 8% on rumours of possible sporting penalties, a Milan-based trader told Reuters.
Italy's tax police on Wednesday searched and seized evidence from the headquarters of the Rome-based club, prosecutors in the town of Tivoli, near Rome, said in a statement.
Lazio said in a statement it was confident that "any misunderstandings or doubts" related to the alleged illicit actions would be cleared up quickly.
The offices of fellow Serie A club Salernitana, which used to be owned by Lazio chairman Claudio Lotito, were also searched as part of the Tivoli investigation.
Salernitana said it would work with authorities but noted that its current owners had nothing to do with the deals under investigation, dating to 2017-2021.
Lotito sold the southern Italian club in January 2022.
A separate investigation by Rome prosecutors, announced at the same time, led to more tax police inspections and seizures at Roma, the city rivals to Lazio.
Roma denied any wrongdoing and said it was "cooperating with the competent authorities and hopes that full clarity will be provided on the matter as soon as possible".
Rome and Tivoli prosecutors said they ordered the seizure of documents related to transfer deals at Lazio, Roma and Salernitana, as well as on the methods the clubs used to set transaction prices.
The investigations follow a probe launched by prosecutors in Turin into alleged false accounting on players' transfers that in January led to a sports court docking Juventus, Italy's most successful soccer club, 15 points this Serie A season.
By 1049 GMT, Lazio's shares were down by 6.7%, underperforming a 0.8% uptick in Milan's all-share index.