The best-selling writer is said to be "deeply distressed" after discovering pictures of her eight-year-old daughter splashed across three pages of OK! magazine.
The snaps were taken while the pair holidayed on the island of Mauritius.
The pictures show young Jessica playing on a private resort beach.
A spokeswoman for Rowling said: "Ms Rowling has taken every possible measure over the last four years to protect her daughter's privacy and ensure that her life remains undisturbed by press intrusion.
"Ms Rowling's lawyer, Derek Currie of Burness, has lodged a formal complaint against OK! magazine with the Press Complaints Commission on her behalf."
The pictures also apparently show Rowling on a beach wearing a bikini, accompanied by a male companion.
OK! publishers Northern and Shell has reported it will investigate the complaints made against the magazine.
A spokesman said: "We shall examine the substance of the complaint and we shall naturally respond appropriately."
The is the second time in a week that Rowling has been spurred into taking action against the media.
Denial
She wrote a letter to The Scotsman newspaper attacking its claims that she was suffering writer's block.
The paper alleged she was suffering from a lack of inspiration for the fifth instalment of the Harry Potter series.
But Rowling replied this was certainly not the case and she was happily writing away.
She said she had made it quite clear there was never any intention to publish the next book in 2001 and that no deadline had been set.
Rowling has spoken before about knowing the storylines for all the books in the planned series of seven.
Earlier this year, Rowling published two special Harry Potter books in aid of Comic Relief.
The big screen adaptation of Harry Potter and the Philosopher¿s Stone is due out at the end of the year.