One woman posted to the bank's Facebook page that she "nearly had a heart attack" after seeing the double transactions on her account.
Others complained of seeing a double up in mortgage payments or insurance payments go out on Friday.
Another couple got a shock to see their first mortgage payment go out twice.
"Our first ever mortgage repayment was duplicated this morning and I freaked out a little."
In a statement on its Facebook page, Westpac New Zealand said some customers were experiencing missing or duplicated transactions on their Westpac One timelines.
"The balance available, however, remains correct. We are aware of the issue and our tech team is working hard to fix this. We apologise for any inconvenience."
A spokesman from the bank today confirmed that there was a problem with transactions.
"An issue has been identified that means some transactions for some customers are appearing as duplicates in their transaction record," the spokesman said.
"The issue does not affect customer balances or the funds available to them. We're working hard to remove the duplicate records and hope to have the issue resolved this morning. We apologise to customers for any inconvenience."
But some customers disputed the fact that their balances were correct.
"Balance is definitely not correct! Great to give updates but the correct information would be good," one woman said.
Others also said their balances were not current and were worried they would now not have enough money in their accounts to cover other payments.
"My balance is not correct either and still payments to come out. According to my balance not enough money there to cover. What will the bank do about covering these payments if error not fixed as was definitely money there to cover. Worrying when on a limited income."
Some expressed delight at seeing their pay come in twice.
"Best pay day ever! Until I read this." said one Facebook poster.
A Westpac spokesman could not immediately say how many customers were affected.
Some customers said they were happy that Westpac were onto the error although they would like to have seen communication sooner from the bank.
Westpac is not the only bank to see payment glitches.
Last year BNZ had intermittent payment issues that spanned on and off over five days.
