Sean Murphy said his photos showed “the real bomber” – the magazine cover was “hurtful” to the victims’ memories and their families.
The images, given to Boston Magazine, show Dzhokhar Tsarnaev with the red dot of a laser sight of a sniper rifle on his face.
The Boston Marathon bombings killed three people.
More than 260 were injured in the two explosions at the marathon finish line on April 15.
Dzhokhar Tsarnaev is also accused of the murder of a fourth person, a university police officer, who was allegedly shot dead by him and his brother Tamerlan in the days after the attack.
A spokesman for state police said the release of the photos had not been authorized, and they would not be given to other news media.
The spokesman also said Sgt Sean Murphy, a police photographer, was subject to an internal investigation.
A tweet from the author of the Boston Magazine article said Sgt Sean Murphy had been “relieved of duty”.
The police photographer told the magazine he released the contrasting images of Dzhokhar Tsarnaev as a response to the Rolling Stone cover.
The latest pictures show the “real Boston bomber, not someone fluffed and buffed for the cover of Rolling Stone magazine”, Sgt Sean Murphy said.
“These were real people, with real lives, with real families,” he said in a statement.
“And to have this cover dropped into Boston was hurtful to their memories and their families.”
The pictures were taken when Dzhokhar Tsarnaev, wounded after a gunfight with police, was found hiding in a dry-docked boat in a residential garden.
On Wednesday, Rolling Stone defended its decision to put Dzhokhar Tsarnaev on the cover, saying it was committed to serious, thoughtful coverage.
But two Massachusetts-based convenience store chains, Rockland and Tedeschi Food Shops, and national pharmacy chains CVS and Walgreens, said they would not stock the edition.
An outpouring of angry comments appeared on social media networks saying the magazine cover was tasteless.
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