Posting on social media, Duncan-Jordan said he was “disappointed” not to have been contacted by the company before the announcement.
“This raises understandable questions around redundancies, the impact on tourism and the offer that the town can make to those of us that live here.
“Businesses are part of our town and need to see themselves in that way, rather than separate entities that have no social responsibilities,” he said.
The company also said it was looking to close the Portsmouth to Le Havre route from October.
Wonnacott told BBC Radio Solent the company has had to make “difficult decisions” following a “drop in demand”.
He said there would be no staff redundancies in the UK.
The firm said it would run a daily service from Portsmouth to Cherbourg in place of the Poole journey.
It added that ships serving Guernsey, Poole and Cherbourg would be allocated to a “more efficient” schedule from 1 November.
This would see its Islander vessel connect Portsmouth to Guernsey, Guernsey to Cherbourg, Cherbourg to Portsmouth.
Its Voyager fast craft will continue to serve Poole to Guernsey, but with the option to travel on to St Malo.