The Irish Hospitality Industry Alliance has insisted the amended smoking ban will not stand up to a legal challenge because of the status of most pub licences.
However, this has been dismissed by a spokeswoman for Minister for Health, Mr Martin.
Mr Finbarr Murphy, an IHIA spokesman, said the vast majority of pubs had received their licences before 1902.
Such a licence covered the entire premises, including the place of dwelling. This meant that gardaí were free to search the public and private areas of the building in cases where people were found drinking after hours.
He said the Department of Health was now trying to distinguish between the public and private areas, so that the smoking ban could be enforced in the public area while the private area remained exempt.
"Our legal advice is that you cannot have one arm of the State viewing it one way, and the other another way," he said. Mr Murphy called on the Minister to immediately publish his legal advice on the issue.
He said the IHIA would not make a decision on whether it would take a legal challenge until it had seen the final version of the regulations and the implementation details.
A spokeswoman for Mr Martin said the Department had received clear legal advice and was not concerned about the licence issue.
On Thursday Mr Martin said smoking would not be banned in hotel rooms, prisons, Garda cells, psychiatric hospitals, nursing homes and hospices.
While doubts still hung over the status of guesthouses yesterday, it was becoming increasingly likely that they would also be exempt from the ban on the basis that almost all the statutory regulations that applied to hotels also applied to guesthouses.
It appeared that bed-and-breakfast establishments would be viewed as private dwelling places and would therefore be exempt from the ban.
The exemptions were described by Action on Smoking and Health (ASH) as "a very disappointing move" . Prof Luke Clancy, the ASH chairman, said the group was disappointed that the ban had been weakened.
He said the exemptions for prisons, hotel bedrooms and certain hospital facilities created a new problem in that employers in these areas had to ensure that they were adequately protecting their employees' health.
The exemptions also questioned the rationale behind protecting the health of certain people, and not protecting the health of others, such as vulnerable people in prison.
Allowing people to smoke in certain areas would also reduce the impact of the cultural shift that was expected when the smoking ban came in, he said.
Meanwhile, the hotel industry welcomed the exemptions as "a practical and welcome solution".
Mr Jim Murphy, Irish Hotels' Federation president, said this removed a major concern for the tourism sector, while still protecting the welfare of staff.
The federation recently met the Minister and proposed a code of practice that would allow smoking in hotel rooms.
The proposals include designated smoking rooms, or smoking floors. Guests would also be asked to refrain from smoking when taking a room-service delivery.
The Vintners' Federation of Ireland said it was becoming increasingly clear that the proposed legislation was "ill thought out and illogical".
"If as the Minister states, the ban is being implemented to protect the health of employees in the workplace, why is he not concerned about the health of prison officers, hotel staff and nursing home staff?" asked Mr Séamus O'Donoghue, VFI's Leinster vice-president.
