Opposition TDs urged the minister to request an investigation following claims gardaí had received alcohol while stationed there, amid other complaints about policing.
Mr Shatter claimed there had been “tourist protesters” who turned up in Mayo when the weather was good and then disappeared.
He told the Dáil: “I regret it is a scandal that €16m of taxpayers money has been utilised to maintain law and order so that people can engage in lawful business engagement in that location.
“It is a waste of public money and resources.”
Wexford TD Mick Wallace argued a complete investigation was needed into allegations about gardaí working there because there was a “blue wall of silence”.
He said that the Garda ombudsman’s hands would be tied without an investigation as provided for under section 106 of Garda legislation.
Requests by the Garda ombudsman for powers to investigate the practices, policies, and procedures of policing in Mayo have previously been denied.
The Independent TD added: “It is not rank and file garda that are causing the problems, it is the people giving them the orders.”
He also argued that the State should not spend €16m defending Shell, the lead energy company overseeing the Corrib gas project.