Thanks for your replies. On both occasions these payments were by cheque, one in an Xmas card and the second in a thank you card when I was leaving.
As my salary was not being paid by the same people I thought that these 2 cash gifts may fall under the 3000 euro yearly allowance for gifts that would be tax exempt?
The problem is that they aren't really a gift though.
It sounds as if they may have been told by their own auditor that the amount was liable to tax, as you were working for them.
I'll put it to you this way - say you know a carpenter, an electrician and a plasterer. And you are building a little conservatory onto your house. And you buy the materials, and the lads supply their labour to you for free because your such a nice guy. And you're so grateful that you give them each a gift of how much they might have charged you for their few days labour... Seeing any problems with this scenario?!
To extend it - What if they were such nice and popular guys, with lots of friends like you, and they work for free all year round, getting lots of "gifts", and only ever paying the low rate of gift tax, rather than higher rate income tax...! Obviously, that just isn't going to fly, as the facts argue against the purported explanation.
OK so my example is a little extreme, but your situation isn't really any different than this ultimately; you were working in their organisation - I would ask the question, if you hadn't been working for them would they still have given you these cheques? Of course not, and therefore the money was given to you in appreciation of work done for them. It's no different than them paying a bonus to a regular employee on their payroll, and that is always subject to tax.
But, the good news is, as an employee, you aren't responsible for discharging the tax; as the employer in this scenario the responsibility for operating PAYE rests with them. And strictly speaking they should have emergency taxed it, if you weren't actually on their payroll. So if they are concerned about dotting the i's and crossing the t's here, they may need to hand over to Revenue an amount of tax equal to 80%-90% of what they paid you, and if anything, you'd then be due a refund!
If you wanna annoy them, suggest that to them and see what they say - ask them to pay the PAYE, PRSI, Income Levy on the grossed up amount of the payments they made to you, and then to issue you with a P60/P45 (it sounds like these payments straddled 2 tax years). There's a good chance they'll just go away then!