There could be about 3,000 teachers on the Government payroll, who are also teaching in private schools.
Sources in the education ministry said this is rampant in schools partnering with the Government to run free secondary education.
The anomaly is likely to be one of the key revelations in the 2012 head count report scheduled to be released in Kampala.
The detailed findings and penalties for such teachers are expected in the new report, sources say.
If confirmed, this will properly explain the massive absenteeism that is eating up the education system. Uganda is one of the countries with the highest level of teacher absenteeism in the world at 35%, according to reports.
Reports show that in most cases, some teachers miss at least two days of work each week.
Sources also revealed that the ministry is still investigating whether these Government teachers are hired on permanent or temporary basis, in the private schools.
"Some private schools had almost their permanent entire staff on the Government payroll. This leaves one wondering whether they ever get time to teach in government schools," a source said.
Investigations indicated that there are hundreds of schools with teachers permanently earning from both government and private institutions.
Efforts to reach top officials at the ministry on the likely penalties to be meted on such teachers were still futile by press time since they were in a top management meeting.
The head count report to be released today is expected to state the number of students who are now under free secondary education. As of last year, at least 600,000 students were getting free secondary education.
The report will also show the progress of free secondary education in the country, achievements and challenges.
It is also expected to highlight the cost implications of educating children under free secondary education this year.
The latest headcount across the country shows a growing number of students joining the programme every year.
In 2007, when the programme started, only 161,396 students were enrolled. The following year, 165,758 joined and another 160,113 in 2009. This year, 201,990 students enrolled.