Loteri Cymru has written to players to inform them of a "system error" which meant not all eligible tickets were included in its monthly Loto+ draw in April, May and June.
It said it was "really sorry for the mistake" and was addressing it by holding an extraordinary Â£15,000 Loto+ draw on Wednesday at 17:00 BST.
The weekly draw was unaffected.
Held on the last Friday of each month, Loto+ is a free draw which includes all non-jackpot wining lottery lines from that month.
Wales' televised lottery has encountered an error just months after its launch.