Dzhokhar Tsarnaev, an ethnic Chechen who came to the U.S. as a child, pleaded not guilty last week while appearing nonchalant.
State police spokesman David Procopio said in a statement that the agency did not authorize the release of the photos to Boston Magazine and will not release them to other media. "The State Police will have no further comment on this matter tonight," he added.
Boston Magazine printed more than a dozen photos from the day Tsarnaev was captured.
Three of the images show Tsarnaev as he emerged from the boat, head bowed, with red smudges and streaks on his clothing and the boat.
Two images show the red dot of the laser sight in the middle of his forehead and just above his left eye. The other show the dot on the top of his head as he buries his face in his arms.
Murphy, who did not return a message from The Associated Press, said in his statement to Boston Magazine that Rolling Stone's cover photo, a softly-lit image of a brooding Tsarnaev, insults officers killed in the line of duty, their colleagues and their families by glamorizing the "face of terror."
"It also could be an incentive to those who may be unstable to do something to get their face on the cover of Rolling Stone magazine," he said.
Rolling Stone has said the cover story on Tsarnaev was part of its "long-standing commitment to serious and thoughtful coverage of the most important political and cultural issues of our day."
In his statement, Murphy said the capture of Tsarnaev played out like a television show, but he hopes his photos show it was "as real as it gets."
"These were real people, with real lives, with real families," Murphy said. "And to have this cover dropped into Boston was hurtful to their memories and their families."
He added: "There is nothing glamorous in bringing more pain to a grieving family."