The 41-year-old suspect was arrested at the church on suspicion of defacing the Ralph Heimans painting that was unveiled last year, The Telegraph reported Thursday.
A Westminster Abbey spokesman said: "In an incident at lunchtime today, a visitor to the abbey sprayed paint on the Ralph Heimans portrait of the Queen presently on display in the Chapter House. Until work can be done to remedy the damage it will, very regrettably, not be possible to have the painting on public view."
Metropolitan Police said: "At approximately 12:30 p.m. today police were called to Westminster Abbey where security guards had detained a 41-year-old man for defacing a painting."
"He was arrested by police on suspicion of criminal damage and taken to a central London police station where he is in custody," police said.