Web users said hacked pictures of her and separate images of fellow actress Amanda Seyfried had been spotted on the dark web, a matrix of encrypted websites that allow users to surf with anonymity.
A representative for Watson confirmed some pictures of her had been stolen, saying they were from a clothes fitting two years ago.
But the spokesman insisted no nude pictures were taken, stating: "Photos from a clothes fitting Emma had with a stylist a couple of years ago have been stolen.
"They are not nude photographs. Lawyers have been instructed and we are not commenting further."
The theft comes amid a row over whether Watson has betrayed feminists by posing partially topless in the magazine Vanity Fair.
In 2015, Watson was threatened with a leak of her personal photos after a speech she gave about gender equality as part of her work as a UN Ambassador for Women.
Speaking at that time, she said: "I knew it was a hoax, I knew the pictures didn't exist, but I think a lot of people that were close to me knew gender equality was an issue but didn't think it was that urgent, that it was a thing of the past.
"And then when they saw that the minute I stood up talking about women's rights I was immediately threatened, I think they were really shocked, my brother was particularly upset."
In September last year, it was reported that Watson had brought in her legal team after website Celeb Jihad published other private photos of her.
The star sent a cease and desist letter after images showing her wearing a sheer top were made public, US website TMZ reported.
The photos argued over in September last year were reportedly taken by Watson's stylist, but were later removed from the web.
That dispute coincided with a public appearance by the star to promote the UN's HeForShe campaign, during which she hailed the possibility of the US electing its first female President.
Last month, a hacker was sentenced to nine months in prison for hacking the electronic accounts of 30 celebrities including Jennifer Lawrence and stealing nude photos and information.
Edward Majerczyk, 29, from Chicago, was also ordered to pay US$5700 in restitution for counseling services for one undisclosed celebrity victim whose photos were disseminated online.