Yahoo, now part of Verizon Communications
However, the company said the investigation indicated that the stolen information did not include passwords in clear text, payment card data, or bank account information.
Yahoo said last December that data from more than 1 billion user accounts was compromised in August 2013.
Verizon in February lowered its original offer by US$350 million for Yahoo assets in the wake of two massive cyber attacks at the internet company.
The closing of the deal, which was first announced in July, had been delayed as the companies assessed the fallout from two data breaches that Yahoo disclosed last year. The company paid US$4.48 billion for Yahoo's core business.
A Yahoo official emphasised Tuesday that the 3 billion figure includes many accounts that were opened but never or only briefly used.
The company said it was sending email notifications to additional affected user accounts.
(Reporting by Munsif Vengattil and David Shepardson,; Editing by Anil D'Silva)