The picture shows two women kissing and lifting their shirts to reveal their torsos with a sign that says "Finland".
"I think the picture is not appropriate, I apologise for it. Such a picture should not have been taken," the 36-year-old prime minister told reporters in Helsinki.
Marin had hit the headlines last week when a video went viral on the internet showing her dancing and partying with her friends.
Comments heard on the video were interpreted by some observers to be a reference to narcotics, which was then strongly debated on social media. Marin denied the allegation.
The PM received a negative result in a drug test that she willingly took to "clear up suspicions" after the video sparked controversy.
"Drug test taken from Prime Minister Sanna Marin on 19 August 2022 did not reveal the presence of drugs. The test was a comprehensive drug test. We did not choose how the test was done," the prime minister's office said in a statement.
Calling the public demand for a drug test "unjust," the PM had said, "I consider these accusations to be very serious, and though I consider the demand for a drug test unjust, for my own legal protection, and to clear up any doubts, I have taken a drug test today, the results of which will come in about a week."
(With inputs from Reuters and The Helsinki Times.)