HMRC are writing to all employers to remind them there is no longer a paper filing option for small firms with fewer than 50 staff members.
Bosses who file their end-of-year return on paper, even well in advance of the 19 May deadline, could receive a penalty.
To file online, employers should register with the Revenue's PAYE Online service and then use the department's free software, purchase commercial software, or appoint an intermediary to file on their behalf.
Assistance is available online and from the taxman's CD-ROM that is sent to all employers.
From May, HMRC will impose new penalties for late payment of PAYE. This includes income tax, National Insurance contributions, student loan deductions and construction industry scheme deductions.
The charges will be between 1% to 5% of the amount paid late. For in-year payments, the percentage charged will increase as the number of late payments in the year rises. See the Revenue's FAQs for more details.