Bosses have apologised to Kirkcaldy pub workers for failing to pay their pension contributions and denied stealing from them.
Deductions were made from wages of employees at the Tipsy Cow and Society but not passed on to their pension fund. Workers have also waited several days for late wages.
Directors Bryan Reid and Hamish Waterson said that they had debt of around £100,000 from the Drummond Hotel, in Markinch, which they previously owned and had fallen behind in payments.
However, they insisted they always intended to pay the dues to pension fund Nest and that wages were never more than seven days late.
The Pensions Regulator was informed and a payment plan has been agreed between the directors, who have 44 employees at the two pubs, and Nest.
One person affected said: “Where has my money gone?
“All staff eligible for pensions are having the same issues.
“Staff have been informed that the problem is being rectified but this should have been rectified when a member of staff raised this issue many months ago.”
Mr Reid said there had been “absolutely no theft” of pension funds from any employee and that Nest was one of his firm’s creditors.
He said: “We have a payment schedule in place with Nest to clear this debt over a period of time.
“This debt must be and will be paid and requires to be by law. There has never been any doubting that fact.
“The pensions of previous and current employees are protected and their pensions will be brought up to date accordingly in time, as agreed.”
He also said that he and Mr Waterson had run Drummonds Hotel at a loss in its final year and kept it trading to protect employees and so it could be sold as a going concern.
During that year, he said, a “seriously tight cash flow” meant employees were sometimes paid late.
Mr Waterson apologised in a letter to employees for any distress caused, telling them that pension dues were always going to be paid and addressing the matter urgently had been accelerated by a media communication.
Nest was set up by the government to ensure every employer has access to a workplace pension scheme which meets pension rules.
A spokeswoman said the company was unable to comment on confidential details relating to employers.
However, she said: “We have a process for reporting employers who do not make pension contributions on time and we follow the same procedure regarding member payments for every employer using Nest.
“This involves four notifications over a 90 day period before reporting them to the regulator.
“Making pension contributions is a legal requirement and we are committed to making sure employers are compliant and members receive the contributions in their accounts that they have worked so hard to earn.”