Kern is accused of attacking 25-year-old Michael Mineo with his baton in October 2008 while two other officers, Alex Cruz and Andrew Morales, allegedly covered up the attack.
Kern testified that he never abused Mineo and that he put the baton away while arresting Mineo. But on cross-examination, Kern said he had first used the baton to hold down the suspect's legs.
Asked by his attorney if he placed the baton in Mineo's rectum, he replied: "No, I did not."
Cruz and Morales have pleaded not guilty to hindering prosecution and official misconduct.
Defense attorneys for the three officers are expected to rest their case following testimony.
They have tried to show that Mineo has, over time, given conflicting accounts of what happened in the subway station.
Closing arguments could begin as early as Monday.