If people see members of the police and military act partially, please report them to authorities," Mr Yudhoyono said in a video message posted on YouTube on Sanday.
Active member of the military and police are not eligible to vote under Indonesia's electoral law.
Mr Prabowo was a Kopassus commander from 1996-98. He served briefly as the head of the Army Strategic Reserves Command in 1998 before being dismissed from the military for his role in the kidnappings.