Shooting on Ek Tha Tiger was disrupted by film industry workers striking over low pay and poor working conditions, reports The Herald.
"They started to shout and stick their placards across the wall at the crew and cast," one source told the newspaper.
The project marks the first time that a Bollywood production crew have shot a feature film in Ireland.
Speaking out against the protesters, a spokesperson said: "They do not represent the majority of those who work full time in the Irish film industry.
"The film platforms Ireland as a location to international filmmakers, as well as breathing life into the Irish film industry, creating jobs in Ireland and generating revenue for the Irish economy."
Zarah Shah, the film's producer, told the newspaper that the production company had earlier faced difficulties in securing Irish visas for the Indian actors and crew.
Actor and 'Being Human' fundraiser Khan, is known to donate a percentage of his earnings to low-paid workers employed in the Hindi film industry in Mumbai.
The Yash Raj Films project will release in June 2012.