Environmental Health Officers have launched a crackdown on cafes offering the traditional Middle Eastern pipes.
Five venues have been fined since March – with at least two hit again after raids last weekend.
Council officials today insisted that the bars, which mostly cater to young Asians, were a "growing problem".
However, the cafe owners today insisted they should be exempt from the smoking ban.
A city council spokesman said: "Staff have visited several premises in the city in relation to alleged indoor shisha smoking in breach of the national smoking ban and have issued a number of fixed penalty notices.
"This appears to be a growing issue and officers are currently taking a closer look at how to approach shisha smoking in smoke-free premises."
Most shisha users smoke flavoured herbs, not tobacco, which contain very little or no nicotine. The water pipes also tend to generate less smoke than cigarettes or cigars.
However, the landmark 2006 ban is on all smoking, not just the smoking of tobacco.
Shisha bar owners protested against the ban and asked for an exemption, which they were not granted.
Councils, however, over the last five years have done little to enforce the law on shisha bars unless they received complaints.
The Evening Times understands that authorities had not been targeting shisha bars as a priority.
However, they have been forced to act following a series of tip-offs from the public.
Shisha bar owners believe such complaints may come from the owners of rival businesses, including cafes that don't have pipes.
But Evening Times sources said the tip-offs have come from Pakistani-born elders in the city's Muslim community.
One of the most popular sisha bars in Glasgow is Cafe Fantoosh, on Commerce Street in Tradeston.
Opened six months ago by business partners Sufi Yousaf and Imran Ali, both 25, it mostly caters for a mixed crowd of students, not all of whom smoke the 'hubble-bubble' pipes.
It has received two £150 fines over recent weeks and now expects to face more serious prosecutions.
Mr Ali said: "We only opened six months ago and didn't realise the smoking ban affected us because we don't use tobacco.
"In fact, when the council officers turned up to fine us they were surprised to find our customers smoking cigarettes outside. That is because we don't allow any tobacco smoking in our cafe."
Fantoosh has a strict over-18 policy and serves soft drinks and cakes as well as shisha pipes, which cost up to £12 each to rent and are usually shared by two or three people.
It smells slightly of fruit rather than stale smoke – thanks to the aromatic herbs smoked in the pipes.
Mr Yousaf said: "We are so busy at weekends we have 10 members of staff working.
"Most of the people who come here are students and most of them are Asians but we get a mix too."
Mr Yousaf and Mr Ali, however, acknowledge that, while they can probably afford to pay the odd fixed-penalty notice, they would probably close if they faced a full-scale prosecution for flouting the smoking ban.
Customers, meanwhile, couldn't understand why there should be a crackdown.
Makrina Aziz, an 18-year-old pharmacy student who has just moved to Glasgow from Kirkcaldy in Fife, said she reckoned Fantoosh was just a cooler version of Starbucks.
The non-smoker said: "There is nobody in here who doesn't want to be and if you don't want to smoke, you don't have to."