Almost half of these were investigated for financial irregularities and six people left when conflicts of interests were discovered.
There are five investigations ongoing into employees and one file is with gardaí.
Details released from the tax authority revealed criminal charges have already been brought against two workers. One person received a three-year sentence. In June 2012, a former staff member was fined €1,500 after pleading guilty to theft.
From 2009 to the end of 2013, 89 workers were sanctioned for incidents of misconduct.
The bulk of these (47 cases) were relatively minor and resulted in formal warnings.
However, in the other categories 42 people either lost their jobs or had their pay cut because of conflicts of interest, financial issues or inappropriate access to data stored by the Revenue Commissioners. There were 12 serious cases of employees improperly accessing data held by the organisation.
Revenue said that in most cases there was more than one type of misconduct involved but the records only reflect the primary offence.
Investigation panels have been appointed in 18 cases between January 2012 and the middle of last month.
Of these, three people have been sacked, one resigned, eight had their pay cut and six inquiries are ongoing.
The details were released by the Revenue Commissioners under the Freedom of Information Act. It said while it takes every allegation seriously the number of inquiries within a workforce of 6,135 remained “relatively small”.
Revenue said all serious cases are dealt with by its human resources unit but it also has a panel of experienced staff to conduct internal investigations.
It said it would not disclose specific details in relation to the cases, the time they happened or anything which would allow the individuals involved to be identified.
It said there was no way of publishing some information about the investigations without “a real and substantive risk of jeopardising” its duty of care to staff.
“We are obliged to apply a high level of confidentiality to data relating to disciplinary code cases and indeed all data relating to Revenue employees or customers,” it said.
In terms of the most serious allegations made in recent years, nine cases of financial irregularities involving staff have been closed since 2009.
None of the people involved are still working in the organisation having been sacked or left of their own accord.
In November 2008 one tax official pleaded guilty to 24 counts of dishonestly using her computer for deception, and was given a two-year suspended sentence.
The papers revealed she has repaid Revenue €108,000 since her crimes were identified.