Cork County VEC got involved in a €162,000 computer scheme but the project was not completed and value was not had, according to Comptroller and Auditor General John Buckley.
Mr Buckley also said that procurement processes had not been correct.
He was speaking before the Public Accounts Committee, which is considering the accounts of Kildare VEC for 2010, Cork City VEC for 2009 and Cork County VEC for 2008.
Joan Russell, CEO of Cork County VEC, said they had introduced a more transparent accounting system and new procurement practices now.
Ms Russell said despite the losses in the €162,000 scheme, computer hardware and software from the project worth €99,000 is in use, though not for the purpose it was originally intended.
In the case of Cork City VEC, Mr Buckley said they had overstaffed and proper procurement practices had not been followed there either in some cases.
He said Kildare VEC also showed shortcomings in its procurement processes.
Cork City VEC CEO Ted Owens said the incorrect enrolment figures and procurement practices, both of which have been criticised, are regrettable.
He said they have now adopted an online enrolment system.
Sean Ashe, CEO of Kildare VEC, said the population of the area had increased hugely over a 10 year period and there were extra demands on the educational system.
He said there was an increase in budget, staff and expenditure as a result, while there had also been an urgent need to build new schools.
Sinn Féin claims 'maladministration' of EU fund money
Separately at the meeting Sinn Féin's Mary Lou McDonald asked about what she called the "maladministration" of money made available to Ireland from the EU Globalisation Fund.
The Irish Government had gained access to money from the fund to help re-train people who lost their jobs, such as those at Dell, SR Technics and Waterford Crystal.
Secretary General at the Department of Education Brigid McManus said she did not accept the word "maladministration" and said there were complexities in administration around the fund.
Ms McManus said the allocation given from the fund was €93m but the actual costs were less than the estimates, she said, which is why money was ultimately sent back to the EU.
Ms McDonald asked why the entire fund had not been used and said that not enough consultation took place in the case of Dell and SR Technics.
Ms McManus said some consultation had taken place but it may not have been structured enough.
She said the engagement with those groups prior to putting in the application for the funds to the EU is always difficult and in hindsight may not have been done as well as it should have.
Deputy McDonald said money was returned to the EU by the Department of Education because of faulty estimates based on insufficient consultation.
She said it sounded like maladministration, in the sense that there were a lot of people who needed to be retrained and yet funds that could have facilitated this were sent back to the EU.
