But while they deal with that for the last time, employers also have to contend with bedding down the new system, which relies on employees being accurately taxed at source.
Just over 12,000 employers with annual PAYE deductions of more than $100,000 a year will be required to file their monthly returns electronically, of whom 1600 have been exempted from the requirement until next year.
The other 175,000 employers will continue to file on paper unless they opt to do so electronically. "Over 50 per cent \[of the 10,500 larger employers\] have done everything they are required to do and downloaded the software," Mr Foubister said.
"There are one or two little issues with the system that we are having to call people back on. But the majority of the people contacting us just need to be helped step by step through the process."
The deadline for their first monthly filing is May 5. Normally a late filing would attract a penalty of $250 but the IRD has said it will waive that except in cases of blatant non-compliance.
The chief executive of the Employers and Manufacturers Association, Alasdair Thompson, said that after hearing a number of horror stories from employers, he had written to Revenue Minister Bill English four weeks ago detailing their problems and seeking assurances.
The letter had yet to be acknowledged.