The university’s Castle Mill development prompted complaints from protesters who say the five-storey building blocks the view of Oxford’s dreaming spires.
Mr Pullman, author of the His Dark Materials trilogy, said: “I feel the buildings are too high.
“I don’t think they would have been approved if it had been known they would be this tall.”
The Cumnor author has become involved in a number of local campaigns, including the fight for the Jericho boatyard, and was branded a “leftie” by former county council leader Keith Mitchell for his campaign against library closures.
He said: “Little by little all the area along the canal has built up and it is gradually losing the rural character that it used to have.”
The Castle Mill development in Roger Dudman Way received planning permission last February, but last month city councillors admitted they don’t like how it looks.
They have now pleaded with Oxford University to demolish the top of the half-finished buildings, despite risking a £1m compensation bill.
University spokesman Matt Pickles said: “We acted in good faith throughout this process. A review conducted by Oxford City Council planning officers confirmed this.”