The department started calling customers about two-step verification in January.
This requires that people enter a security code when they log in, to verify their identity.
It had made 47,000 calls by the end of February and set up two-step verification (2SV) for almost 10,000 people.
IRD deputy commissioner James Grayson said some people had questioned IR's callers' identity and were concerned they were being targeted by scammers.
"It's good they're being vigilant.
"From now on, before we call, we'll send a secure message to customers via their myIR accounts explaining how to set up 2SV. And we will only call customers who have not set up 2SV after they received the message.
"We're keen to talk to people who may not have had much recent contact with Inland Revenue, or who may only look at their myIR once a year, so they know about the improved security two-step verification brings."
He said people could cross-check the number on a caller ID against the phone numbers on its website.
They could also request that they be sent a web message to verify that it was the department calling.
"When we call, we won't ask people to click on a link to get to their accounts to make the necessary 2SV changes. We're also not asking for personal information such as credit card or bank account details and we won't be asking people to pay anything.
"We won't use intimidating language or threaten sudden arrest or pressure anyone to act immediately, without warning. We will never ask for passwords."
