Pralhad Kolhe has ordered fishermen not to use Cove Harbour, but he was told to remove boulders blocking access to the harbour by the council in January.
New boulders across the road to the site have now been installed.
The fishermen have collected more than 9,500 signatures on a petition and raised Â£3,300 to fund a legal campaign.
Locals say the harbour has been used for fishing for hundreds of years, but the landowner insists boat owners have "no right" to store their equipment on his property.
The dispute dates back to April 2014, when Mr Kolhe issued a legal notice to the fishermen ordering them to remove their boats from the beach.
A further notice was issued in September 2015 after the fishermen insisted they would be staying put, before the boulders were put up blocking off the pier in December.
Council officials wrote to Mr Kolhe in January about the boulders, but on Saturday new stones were seen being placed across the access road.
Mr Kolhe's representatives have not yet responded to a BBC Scotland request for a comment on the dispute.
New boulders have been placed at the entrance of a small Aberdeen harbour in an ongoing row between fishermen and the landowner.