Tui, owner of Thomson and First Choice, was fined 48 times during 2015 and 2016 by the travel association Abta.
The breaches included inaccurate advertising and sending holidaymakers to resorts where significant building work was being carried out.
Tui said it was committed to resolving any issue a customer experiences.
The figures, compiled from industry data by You & Yours on Radio 4, show Tui's most recent fine of £1,500 was imposed in December 2016 for cancelling a customer's travel arrangements after the holiday had already been paid for in full.
Many of the other fines were for failing to respond quickly enough to correspondence.
However, three of them were for not telling customers about significant building works at their resorts before they went on holiday.
Abta's code of conduct states customers should be told about building work in advance, or offered alternative travel arrangements or a full refund if the alternative would constitute a significant alteration to their holiday.
Despite being fined, Tui has continued to send some holidaymakers to building sites without warning.
In November 2016, Keith Parkins from Guildford in Surrey went to Tenerife with Tui's company Thomson. He arrived to find significant construction work underway at his hotel.
"The arrival was, to put it bluntly, a shock," he said. "Coming down the hill, the first thing you could see was the long sun terrace, digger, bulldozer, piles of rubble, workmen, wheelbarrows, you name it. Inside, most of the hotel was taped off.
The very first morning, I was woken up after 07:00 by the horrendous racket of pneumatic drills. It was just unbelievable."
Thomson has offered Mr Parkins a £250 refund or a £345 travel voucher. He thinks it is insufficient, as he paid £1,762 for his holiday and is not keen on travelling with the company again.
Other firms fined for breaches of the Abta code include Tui's biggest rival, Thomas Cook.
It was fined on 24 occasions during 2015 and 2016, often for failing to deal with customer's complaints or for not paying arbitration awards on time.
In total, it was charged £10,750. Tui was fined a total of £38,500 over the same period.
"You really need to look at the percentage of problems you are seeing in terms of the total number of people they take away," said Sean Tipton from Abta.
"If it is just a one-off problem, obviously that's not good enough for you as the holidaymaker, but it doesn't necessarily represent a systemic problem with the company."
In a statement, Tui said the vast majority of its customers have a "great holiday", adding: "We are sorry to hear if a holiday falls short of expectations or is impacted by circumstances, which are sometimes beyond our control. We remain committed to resolving any issue a customer experiences."
Thomas Cook said: "We aim for zero breaches of the Abta code and we continue to improve the business and put our customer at the heart of everything we do."
"We would like to see no breaches of the code as well," said Abta's Sean Tipton.
"The point is, when they do occur, it is essential the tour operator does their best to address it straight away, or if it is not resolved satisfactorily, then people should come and tell us about it."
The UK's biggest tour operator has been repeatedly fined for failing to stick to the travel industry's own code of conduct.